Compositions comprising bacterial strains

ABSTRACT

Provided are compositions comprising a bacterial strain of the genus  Blautia , for use in a method of increasing the microbiota diversity and/or inducing stability of the microbiota of a subject.

CROSS-REFERENCE

This application is a continuation of U.S. application Ser. No.15/915,889, filed Mar. 8, 2018 which is a continuation of InternationalApplication No. PCT/GB2017/053722, filed Dec. 12, 2017, which claims thebenefit of Great Britain Application No. 1621123.7, filed Dec. 12, 2016;all of which are hereby incorporated by reference in their entirety.Further, all publications, patents, and patent applications mentioned inthis specification are herein incorporated by reference in theirentirety to the same extent as if each individual publication, patent,or patent application was specifically and individually indicated to beincorporated by reference.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Dec. 7, 2017, isnamed p069516_sequence_listing.txt and is 12,288 bytes in size.

TECHNICAL FIELD

This invention is in the field of compositions comprising bacterialstrains isolated from the mammalian digestive tract and the use of suchcompositions in the treatment of disease.

BACKGROUND TO THE INVENTION

The human intestine is thought to be sterile in utero, but it is exposedto a large variety of maternal and environmental microbes immediatelyafter birth. Thereafter, a dynamic period of microbial colonization andsuccession occurs, which is influenced by factors such as delivery mode,environment, diet and host genotype, all of which impact upon thecomposition of the gut microbiota, particularly during early life.Subsequently, the microbiota stabilizes and becomes adult-like [1]. Thehuman gut microbiota contains more than 1500 different phylotypesdominated in abundance levels by two major bacterial divisions (phyla),the Bacteroidetes and the Firmicutes [2]. The successful symbioticrelationships arising from bacterial colonization of the human gut haveyielded a wide variety of metabolic, structural, protective and otherbeneficial functions. The enhanced metabolic activities of the colonizedgut ensure that otherwise indigestible dietary components are degradedwith release of by-products providing an important nutrient source forthe host and additional health benefits. Similarly, the immunologicalimportance of the gut microbiota is well-recognized and is exemplifiedin germfree animals which have an impaired immune system that isfunctionally reconstituted following the introduction of commensalbacteria [3-5].

Dramatic changes in microbiota composition have been documented ingastrointestinal disorders such as inflammatory bowel disease (IBD). Forexample, the levels of Clostridium cluster XIVa bacteria are reduced inIBD subjects whilst numbers of E. coli are increased, suggesting a shiftin the balance of symbionts and pathobionts within the gut [6-9,18].

In recognition of the potential positive effect that certain bacterialstrains may have on the animal gut, various strains have been proposedfor use in the treatment of various diseases (see, for example,[10-13]). A number of strains, including mostly Lactobacillus andBifidobacterium strains, have been proposed for use in treating variousbowel disorders (see [14] for a review and see [15]). Reference [16]proposes the use of strains of the genus Blautia for use in modulatingthe microbial balance of the digestive ecosystem. In the context ofreference 16, modulation refers to promoting the activity of theacetogenic bacterial flora to the detriment of methanogenic and sulfurreducing bacteria. This document therefore teaches only an increase inacetogenic bacteria. There is no discussion relating to the diversity ofspecies belonging to a number of taxa. Reference [17] discusses the useof Blautia for improving survival in patients affected by graft versushost disease (GVDH). It mentions that increased bacterial diversity isassociated with reduced GVDH-related mortality and that increasedamounts of bacteria of the Blautia genus were associated with reducedGVDH. However, there is no suggestion that the administration of Blautiato a patient effects an increase in microbiota diversity and/or inducesstability of the microbiota in a subject.

The relationship between different bacterial strains and differentdiseases, and the precise effects of particular bacterial strains on thegut and at a systemic level and on any particular types of diseases, arepoorly characterised and results to date are variable and pose morequestions than provide answers [18].

A hallmark of many human diseases linked to microbiota alteration isloss of microbiota diversity. As distinct from so-called dysbiosis whichis simply an altered microbiota composition compared to the typicalaggregate microbiota in healthy subjects, loss of microbiota diversitymay be quantified by a measurable reduction in number of thesequence-based bacterial classifications or Operational Taxonomic Units(OTUs) in a sample, typically determined by 16S rRNA amplicon sequencingmethods. Loss of diversity is also measured by reductions in the ShannonDiversity Index, or the Chao index. Reduced microbiota diversity isreported in recent studies of obesity, inflammatory bowel disease (IBD),irritable bowel syndrome (IBS), type 2 diabetes and frailer older people[20]. Re-establishing the healthy microbiota can be difficult as thebacteria in the gut are resistant to colonisation. This poses achallenge when trying to treat the microbiota of unhealthy subjects byincreasing the diversity of the microbiota [19]. The accompanying lossof microbial metabolic function is assumed to be a contributory factorto the symptoms of these pathophysiologies. In contrast to healthyadults in whom the microbiota is stable, the microbiota of unhealthysubjects such as those suffering IBD, IBS and frail elderly subjects isunstable [18, 20].

There is a requirement for the potential effects of gut bacteria to becharacterised so that new therapies using gut bacteria can be developed.

SUMMARY OF THE INVENTION

The inventors have developed new therapies for treating and preventingdiseases and disorders by increasing or maintaining the intestinalmicrobiota diversity in a subject. In particular, the inventors haveidentified that bacterial strains from the genus Blautia can beeffective in increasing or maintaining the number and/or evenness ofdifferent types of bacteria in the distal gut of a subject. As describedin the examples, oral administration of compositions comprising Blautiahydrogenotrophica increases the microbiota diversity in stool. Thisincrease in diversity was seen in healthy and IBS subjects. However, IBSsubjects receiving placebo had a statistically significant reduction inmicrobiome diversity during the course of the study. Additionally, theexamples show that treatment with compositions comprising Blautiahydrogenotrophica, but not placebo, increased the stability of themicrobiota in IBS subjects throughout the course of the study. Thestability of the microbiota in subjects receiving the compositioncomprising Blautia hydrogenotrophica was comparable to that of healthycontrol subjects.

Therefore, in a first embodiment, the invention provides a compositioncomprising a bacterial strain of the genus Blautia, for use in a methodof increasing or maintaining the microbiota diversity. Similarly, thereis also provided a method of increasing or maintaining the microbiotadiversity in a subject comprising use of a bacterial strain of the genusBlautia.

The term “increasing or maintaining the microbiota diversity” is usedherein to mean increasing or maintaining the number of different typesof bacteria and/or the evenness of the different types of bacteria inthe microbiota of a subject. In some embodiments, the microbiotadiversity is increased. In some embodiments, the number of differentgenera of bacteria in the microbiota is increased. In some embodiments,the number of different species of bacteria in the microbiota isincreased. In some embodiments, the number of different strains ofbacteria in the microbiota is increased. In some embodiments, themicrobiota diversity is maintained. In some embodiments, the number ofdifferent genera of bacteria in the microbiota is maintained. In someembodiments, the number of different species of bacteria in themicrobiota is maintained. In some embodiments, the number of differentstrains of bacteria in the microbiota is maintained. In someembodiments, the number of genera, species and strains in the microbiotais increased or maintained.

The increase in microbiotia diversity may be for non-acetogenicbacteria. It may also be for both acetogenic and non-acetogenicbacteria. Such bacteria are well known in the art. Briefly, acetogenicbacteria produce acetate as an end product of anaerobic respiration orfermentation.

In some embodiments, loss, increase or maintenance of microbiotadiversity may be quantified by a measurable reduction, increase ormaintenance, respectively, in the number of the sequence-based bacterialclassifications or Operational Taxonomic Units (OTUs) in a sample,typically determined by 16S rRNA amplicon sequencing methods. In someembodiments, loss of diversity may be measured by reductions in theShannon Diversity Index, or the Chao index. Conversely, in someembodiments, an increase of diversity may be measured by an increase inthe Shannon Diversity Index, or the Chao index. Similarly, in someembodiments, maintenance of diversity may be measured by the same resultin the Shannon Diversity Index, or the Chao index.

In some embodiments, the evenness of the different types of bacteria isincreased. In some embodiments, the relative abundance of the differenttypes of bacteria in the microbiota becomes more even followingtreatment or prevention with a composition of the invention.

The inventors have also developed new therapies for treating andpreventing diseases and disorders by inducing stability of theintestinal microbiota. In particular, the inventors have identified thatbacterial strains from the genus Blautia induce stability of theintestinal microbiota. By “induce stability” is meant that themicrobiota diversity remains stable and also the relative numbers of thedifferent Genus in the microbiota remains stable. This is important as anumber of diseases and disorders, including IBS and IBD, arecharacterised by reduced stability of the microbiota. As described inthe examples, oral administration of compositions comprising Blautiahydrogenotrophica induces stability of the microbiota in stool.Therefore, in a further embodiment, the invention provides a compositioncomprising a bacterial strain of the genus Blautia, for use in a methodof inducing stability of the microbiota in a subject. Similarly, thereis also provided a method of inducing stability of the microbiota in asubject comprising use of a bacterial strain of the genus Blautia.

In some embodiments, the relative numbers of the different bacterialspecies in the microbiota of a subject becomes more stable followingtreatment or prevention with a composition of the invention, for examplein a subject diagnosed with a disease or disorder characterised by areduction in the diversity of microbiota. In some embodiments, therelative numbers of the different bacterial Genus in the microbiota of asubject becomes more stable following treatment or prevention with acomposition of the invention, for example in a subject diagnosed with adisease or disorder characterised by a reduction in the diversity ofmicrobiota. The stability of a subject's microbiota can be assessed bycomparing the microbiome from the subject at two different time points.If there is a difference in the microbiome, this can be indicative ofdisease or of a disorder being present. In some embodiments, the twodifferent time points are at least three days apart (e.g. at least 1week, 2 weeks, 1 month, 3 months, 6 months, 1 year, 2 years apart). Insome embodiments, the two different time points are 3-7 days apart, 1-2weeks apart, 2-4 weeks apart, 4-8 weeks apart, 8-24 weeks apart, 24-40weeks apart, 40-52 weeks apart or more than 52 weeks apart. In someembodiments, more than two different time points are used, e.g. three,four, five or more than five time points. Suitable intervals are chosenbetween the various time points, for example, as set out above.

In preferred embodiments of all aspects of the invention, the bacterialstrain is of Blautia hydrogenotrophica and is preferably the bacteriumdeposited under accession number DSM 10507/14294.

In some embodiments, the microbiota diversity and/or the stability ofthe microbiota refers to the microbiota diversity and/or the stabilityin stool in the subject. In some embodiments, the microbiota diversityand/or the stability of the microbiota refers to the microbiotadiversity and/or the stability in a stool sample from the subject. Insome embodiments, the microbiota diversity and/or the stability of themicrobiota refers to the microbiota diversity and/or the stability inthe distal gut of the subject. In some embodiments, the microbiotadiversity and/or the stability of the microbiota refers to themicrobiota diversity and/or the stability in the gastrointestinal tractof the subject. In some embodiments, the microbiota diversity and/or thestability of the microbiota refers to the microbiota diversity and/orthe stability in the caecum. In some embodiments, the microbiotadiversity and/or the stability of the microbiota refers to themicrobiota diversity and/or the stability in the colon.

In some embodiments, the invention provides a composition comprising abacterial strain of the genus Blautia, for use in a method of treatingor preventing a disease or disorder associated with a level ofmicrobiota diversity that is reduced relative to the microbiotadiversity of a healthy subject. In some embodiments, the treatment orprevention using a composition of the invention results in themicrobiota diversity increasing to the levels present in a healthyindividual. In some embodiments, treatment or prevention using acomposition of the invention results in the microbiota diversityincreasing to levels greater than those present in some healthyindividuals. In some embodiments, the healthy individual is of asimilar/same age to the subject and/or is of a similar/same race to thesubject. Similarly, the invention also provides a method of treatment orprevention of a disease or disorder associated with a level ofmicrobiota diversity that is reduced relative to the microbiotadiversity of a healthy subject wherein the method comprisesadministering a composition comprising a bacterial strain of the genusBlautia. Examples of diseases or disorders associated with a reducedlevel of microbiota diversity include but are not limited to: IBS, IBD[21], obesity [22], type 2 diabetes, infectious diseases, allergicdiseases, autoimmune diseases and metabolic diseases/disorders.Treatment or prevention of these diseases and disorders is encompassedby the invention. In some embodiments, the disease or disorder is IBS.

In some embodiments, the subject is an infant or child with a reducedmicrobiota diversity compared to a healthy infant or child,respectively. It has been observed that some children who develop anallergic disease later in life have a reduced diversity of faecalmicrobiota as 1 week old infants [23]. Thus, in some embodiments, theinfant is less than 1 week old, is less than 2 weeks old, is less thanone month old, is less than two months old or is less than four monthsold. In some embodiments, the subject is an infant who has not beendelivered via a vaginal birth. For example, in some embodiments, thesubject is an infant who has been delivered by Caesarean section.Reduced microbiota diversity has also been reported in frail elderlysubjects. In some embodiments, therefore, the subject is an elderlysubject, for example, a frail elderly subject. In some embodiments, thesubject is 65 or more years in age (e.g. 70 or more, 75 or more, 80 ormore, 85 or more or 90 or more years in age) [20].

It has been estimated that a single human individual has approximately101 different bacterial species and 195 different strains in itsmicrobiota [24]. Accordingly, in some embodiments, the composition isfor use in treating a subject having less than 101 different bacterialspecies (e.g. less than 100, 99, 98, 97, 96, 95, 94, 93, 92, 91, 90, 85,80, 75 or 70 bacterial species) and/or less than 195 different strains(e.g. less than 194, 193, 192, 191, 190, 189, 188, 187, 186, 185, 183,180, 175, 170, 165, 160, 150, 140 bacterial strains) in its microbiota.In some embodiments, the treatment or prevention results in themicrobiota diversity increasing to more than 80 bacterial species (e.g.more than 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100 bacterialspecies) or to 101 bacterial species. For example, in some embodiments,the treatment or prevention results in the microbiota diversityincreasing to more than 90 bacterial species. For example, in someembodiments, the treatment or prevention results in the microbiotadiversity increasing to more than 95 bacterial species. For example, insome embodiments, the treatment or prevention results in the microbiotadiversity increasing to more than 97 bacterial species. For example, insome embodiments, the treatment or prevention results in the microbiotadiversity increasing to more than 99 bacterial species. In someembodiments, the treatment or prevention results in the microbiotadiversity increasing to more than 160 bacterial strains (e.g. more than165, 170, 185, 186, 187, 188, 189, 190, 191, 192, 193 or 194 bacterialspecies) or to 195 bacterial strains. For example, in some embodiments,the treatment or prevention results in the microbiota diversityincreasing to more than 175 bacterial strains. For example, in someembodiments, the treatment or prevention results in the microbiotadiversity increasing to more than 185 bacterial strains. For example, insome embodiments, the treatment or prevention results in the microbiotadiversity increasing to more than 190 bacterial strains.

In some embodiments, the treatment or prevention results in themicrobiota diversity increasing by at least one bacterial genus (e.g. byat least two, three, four, five, six, seven, eight, nine or tenbacterial genera). In some embodiments, the treatment or preventionresults in the microbiota diversity increasing by at least one bacterialspecies (e.g. by at least two, three, four, five, six, seven, eight,nine, ten, 12, 15, 17 or 20 bacterial species). In some embodiments, thetreatment or prevention results in the microbiota diversity increasingby at least one bacterial strain (e.g. by at least two, three, four,five, six, seven, eight, nine, ten, 12, 15, 17, 20 or 25 bacterialstrains).

In some embodiments, the invention provides a composition comprising abacterial strain of the genus Blautia, for use in a method of treatingor preventing a disease or disorder associated with reduced stability ofthe microbiota compared to the stability of the microbiota in a healthysubject (or compared to a population of healthy subjects). By “reducedstability of the microbiota” is meant that the microbiota diversity doesnot remain as stable and also the relative numbers of the differentGenus in the microbiota do not remain as stable as the stabilityobserved in a healthy subject or in a population of healthy subjects. Insome embodiments, inducing stability of the microbiota results in thestability being induced to a similar level as is present in a healthysubject, or in a population of healthy subjects. In some embodiments,inducing stability of the microbiota results in the stability beinginduced to the same level as is present in a healthy subject, or in apopulation of healthy subjects. Similarly, the invention provides amethod of treating or preventing a disease or disorder associated withreduced stability of the microbiota wherein the method comprisesadministering a composition comprising a bacteria strain of the genusBlautia. For example, the pathogenesis of some diseases or disorders ischaracterised by reduced stability of the microbiota. Examples of suchdiseases and disorders are IBS, IBD, diabetes (e.g. type 2 diabetes),allergic diseases, autoimmune diseases and metabolic diseases/disorders.Accordingly, in some embodiments, the invention provides a compositioncomprising a bacterial strain of the genus Blautia, for use in a methodof treating or preventing a disease or disorder associated with reducedstability of the microbiota, wherein the treatment or preventioncomprises inducing stability of the microbiota. In some embodiments, thedisease or disorder is selected from IBS, IBD, diabetes (e.g. type 2diabetes), allergic diseases, autoimmune diseases and metabolicdiseases/disorders. In some embodiments, the disease or disorder is IBSor IBD. In some embodiments, the disease or disorder is IBS.Accordingly, in some embodiments, the invention provides a compositioncomprising a bacterial strain of the genus Blautia, for use in a methodof treating or preventing IBS or IBD, wherein the treatment orprevention comprises inducing stability of the microbiota.

In some embodiments, the invention provides a method of treatment orprevention of a disease or disorder associated with a level ofmicrobiota diversity that is reduced relative to the microbiotadiversity of a healthy subject wherein the method comprises diagnosing asubject as having a reduced level of microbiota diversity and then if areduced level of diversity is found to be present, administering acomposition comprising a bacterial strain of the genus Blautia to thesubject.

In some embodiments, the invention provides a method of treatment orprevention of a disease or disorder associated with reduced stability ofmicrobiota relative to the stability of microbiota in a healthy subjectwherein the method comprises diagnosing a subject as having reducedstability of microbiota and then if reduced stability is found to bepresent, administering a composition comprising a bacterial strain ofthe genus Blautia to the subject.

In preferred embodiments of the invention, the bacterial strain in thecomposition is of Blautia hydrogenotrophica. Closely related strains mayalso be used, such as bacterial strains that have a 16s rRNA sequencethat is at least 97%, 98%, 99%, 99.5% or 99.9% identical to the 16s rRNAsequence of a bacterial strain of Blautia hydrogenotrophica. Preferably,the bacterial strain has a 16s rRNA sequence that is at least 97%, 98%,99%, 99.5% or 99.9% identical to SEQ ID NO:5. Preferably, the bacterialstrain has the 16s rRNA sequence of SEQ ID NO:5. Most preferably, thebacterial strain in the composition is the Blautia hydrogenotrophicastrain deposited under accession number DSM 10507/14294.

In further embodiments of the invention, the bacterial strain in thecomposition is of Blautia stercoris. Closely related strains may also beused, such as bacterial strains that have a 16s rRNA sequence that is atleast 97%, 98%, 99%, 99.5% or 99.9% identical to the 16s rRNA sequenceof a bacterial strain of Blautia stercoris. Preferably, the bacterialstrain has a 16s rRNA sequence that is at least 97%, 98%, 99%, 99.5% or99.9% identical to SEQ ID NO:1 or 3. Preferably, the sequence identityis to SEQ ID NO:3. Preferably, the bacterial strain for use in theinvention has the 16s rRNA sequence represented by SEQ ID NO:3.

In further embodiments of the invention, the bacterial strain in thecomposition is of Blautia wexlerae. Closely related strains may also beused, such as bacterial strains that have a 16s rRNA sequence that is atleast 97%, 98%, 99%, 99.5% or 99.9% identical to the 16s rRNA sequenceof a bacterial strain of Blautia wexlerae. Preferably, the bacterialstrain has a 16s rRNA sequence that is at least 97%, 98%, 99%, 99.5% or99.9% identical to SEQ ID NO:2 or 4. Preferably, the sequence identityis to SEQ ID NO:4. Preferably, the bacterial strain for use in theinvention has the 16s rRNA sequence represented by SEQ ID NO:4.

In certain embodiments, the composition of the invention is for oraladministration. Oral administration of the strains of the invention canbe effective for increasing the microbiota diversity and/or inducing thestability of the microbiota. Also, oral administration is convenient forsubjects and practitioners and allows delivery to and/or partial ortotal colonisation of the intestine.

In certain embodiments, the composition of the invention comprises oneor more pharmaceutically acceptable excipients or carriers.

In certain embodiments, the composition of the invention comprises abacterial strain that has been lyophilised. Lyophilisation is aneffective and convenient technique for preparing stable compositionsthat allow delivery of bacteria, and is shown to provide effectivecompositions in the examples.

In certain embodiments, the invention provides a food product comprisingthe composition as described above.

In certain embodiments, the invention provides a vaccine compositioncomprising the composition as described above.

Additionally, the invention provides a method of increasing themicrobiota diversity and/or inducing the stability of the microbiota andthereby treating or preventing diseases or disorders associated with areduced microbiota diversity and/or with reduced stability of themicrobiota, comprising administering a composition comprising abacterial strain of the genus Blautia.

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1: Comparison of microbiota in healthy and IBS patients.

FIG. 2: Comparison of microbiota diversity between Day 16 and Day 1 forhealthy and IBS patients after treatment with BlautiX or placebo.

FIGS. 3A-3B: FIG. 3A) Interconnectivity of the microbiome in healthypatients at Day 1, Day 16 and end of study after BlautiX treatment, FIG.3B) Interconnectivity of the microbiome in IBS patients at Day 1, Day 16and end of study after BlautiX treatment. The interconnectivity resultsseen on Day 1, Day 16 and at the End of Study for healthy individualsthat are presented in FIG. 3A are also shown in FIGS. 3A1, 3A2 and 3A3,respectively. The interconnectivity results seen on Day 1, Day 16 and atthe End of Study for IBS patients that are presented in FIG. 3B are alsoshown in FIGS. 3B1, 3B2 and 3B3, respectively.

FIGS. 4A-4C: A comparison of the instability in microbiota profiles inhealthy and IBS patients after treatment with BlautiX or placebos atFIG. 4A) Day 16 and Day 1, FIG. 4B) end of study and Day 1 and FIG. 4C)end of study and Day 16.

FIG. 5: Comparison of microbiota diversity at different time points forhealthy and IBS patients after BlautiX treatment.

FIGS. 6A-6B: FIG. 6A) The mutual exclusion network in healthy patientsat Day 1, Day 16 and end of study after BlautiX treatment, FIG. 6B) Themutual exclusion network in IBS patients at Day 1, Day 16 and end ofstudy after BlautiX treatment. The mutual exclusion results seen on Day1, Day 16 and at the End of Study for healthy individuals that arepresented in FIG. 6A are also shown in FIGS. 6A1, 6A2 and 6A3,respectively. The mutual exclusion results seen on Day 1, Day 16 and atthe End of Study for IBS patients that are presented in FIG. 6B are alsoshown in FIGS. 6B1, 6B2 and 6B3, respectively.

FIG. 7: Hierarchical clustering of microbiota.

FIG. 8: Comparison of microbiota profiles before (D14) and after (D32)Blautix treatment based on Bray-Curtis dissimilarities.

FIGS. 9A-9C: (FIG. 9A) Visualization of microbiota profiles of differentgroups at D-14 using PCoA based on Bray-Curtis dissimilarities. (FIG.9B) Visualization of microbiota profiles of the groups at D14 using PCoAbased on Bray-Curtis dissimilarities. (FIG. 9C) Significant difference(p-value=0.002) in the microbiota profiles for the Blautix group wasseen across the timepoints.

FIG. 10: Comparison of microbiota profiles for Blautix treatment atstudy timepoints (D-14, D-1, D34) based on Bray-Curtis dissimilarities.

DISCLOSURE OF THE INVENTION

Bacterial Strains

The compositions of the invention comprise a bacterial strain of thegenus Blautia. The examples demonstrate that bacteria of this genus areuseful for increasing the microbiota diversity and/or inducing thestability of the microbiota. The preferred bacterial strains are of thespecies Blautia hydrogenotrophica, Blautia stercoris and Blautiawexlerae. Most preferred is Blautia hydrogenotrophica, particularly thebacterium deposited under accession number DSM 10507/14294.

Examples of Blautia strains for use in the invention include Blautiahydrogenotrophica, B. stercoris, B. faecis, B. coccoides, B. glucerasea,B. hansenii, B. luti, B. producta, B. schinkii and B. wexlerae. TheBlautia species are Gram-reaction-positive, non-motile bacteria that maybe either coccoid or oval and all are obligate anaerobes that produceacetic acid as the major end product of glucose fermentation [25].Blautia may be isolated from the human gut, although B. producta wasisolated from a septicaemia sample.

Blautia hydrogenotrophica (previously known as Ruminococcushydrogenotrophicus) has been isolated from the guts of mammals, isstrictly anaerobic, and metabolises H₂/CO₂ to acetate, which may beimportant for human nutrition and health. The type strain of Blautiahydrogenotrophica is S5a33=DSM 10507=JCM 14656. The GenBank accessionnumber for the 16S rRNA gene sequence of Blautia hydrogenotrophicastrain S5a36 is X95624.1 (disclosed herein as SEQ ID NO:5). Thisexemplary Blautia hydrogenotrophica strain is described in [25] and[26]. The S5a33 strain and the S5a36 strain correspond to two subclonesof an acetogenic strain isolated from a faecal sample of a healthysubject. They show identical morphology, physiology and metabolism andhave identical 16S rRNA sequences. Thus, in some embodiments, theBlautia hydrogenotrophica for use in the invention has the 16S rRNAsequence of SEQ ID NO:5.

The Blautia hydrogenotrophica bacterium deposited under accession numberDSM 10507 and also under accession number DSM 14294 was tested in theexamples and is also referred to herein as strain BH. Strain BH wasdeposited with the Deutsche Sammlung von Mikroorganismen [GermanMicroorganism Collection] (Mascheroder Weg 1b, 38124 Braunschweig,Germany) on 10 May 2001 as “Ruminococcus hydrogenotrophicus” underaccession number DSM 10507 and also under accession number DSM 14294.The depositor was INRA Laboratoire de Microbiologie CR deClermont-Ferrand/Theix 63122 Saint Genès Champanelle, France. Ownershipof the bacterium deposited as DSM 10507 and DSM 14294 has passed viaassignment to 4D Pharma Plc. The DSM 14294 deposit was made under theterms of the Budapest Treaty. Maintenance of a viable culture is assuredfor 30 years from the date of deposit. All restrictions on theavailability to the public of the microorganisms deposited as DSM 10507and 14294 will be irrevocably removed upon the granting of a patent forthis application.

The GenBank accession number for the 16S rRNA gene sequence of Blautiastercoris strain GAM6-1^(T) is HM626177 (disclosed herein as SEQ IDNO:1). An exemplary Blautia stercoris strain is described in [27]. Thetype strain of Blautia wexlerae is WAL 14507=ATCC BAA-1564=DSM 19850[25]. The GenBank accession number for the 16S rRNA gene sequence ofBlautia wexlerae strain WAL 14507 T is EF036467 (disclosed herein as SEQID NO:2). This exemplary Blautia wexlerae strain is described in [25].

A preferred Blautia stercoris strain is the strain deposited underaccession number NCIMB 42381, which is also referred to herein as strain830. A 16S rRNA sequence for the 830 strain is provided in SEQ ID NO:3.Strain 830 was deposited with the international depositary authorityNCIMB, Ltd. (Ferguson Building, Aberdeen, AB21 9YA, Scotland) by GTBiologics Ltd. (Life Sciences Innovation Building, Aberdeen, AB25 2ZS,Scotland) on 12 Mar. 2015 as “Blautia stercoris 830” and was assignedaccession number NCIMB 42381. GT Biologics Ltd. subsequently changed itsname to 4D Pharma Research Limited. The NCIMB 42381 deposit was madeunder the terms of the Budapest Treaty. Maintenance of a viable cultureis assured for 30 years from the date of deposit. All restrictions onthe availability to the public of the deposited microorganism will beirrevocably removed upon the granting of a patent for this application.

A preferred Blautia wexlerae strain is the strain deposited underaccession number NCIMB 42486, which is also referred to herein as strainMRX008. A 16S rRNA sequence for the MRX008 strain is provided in SEQ IDNO:4. Strain MRX008 was deposited with the international depositaryauthority NCIMB, Ltd. (Ferguson Building, Aberdeen, AB21 9YA, Scotland)by 4D Pharma Research Ltd. (Life Sciences Innovation Building, Aberdeen,AB25 2ZS, Scotland) on 16 Nov. 2015 as “Blautia/Ruminococcus” and wasassigned accession number NCIMB 42486. The NCIMB 42486 deposit was madeunder the terms of the Budapest Treaty. Maintenance of a viable cultureis assured for 30 years from the date of deposit. All restrictions onthe availability to the public of the deposited microorganism will beirrevocably removed upon the granting of a patent for this application.

Bacterial strains closely related to the strain tested in the examplesare also expected to be effective for increasing the microbiotadiversity and/or inducing the stability of the microbiota. In certainembodiments, the bacterial strain for use in the invention has a 16srRNA sequence that is at least 97%, 98%, 99%, 99.5% or 99.9% identicalto the 16s rRNA sequence of a bacterial strain of Blautiahydrogenotrophica. Preferably, the bacterial strain for use in theinvention has a 16s rRNA sequence that is at least 97%, 98%, 99%, 99.5%or 99.9% identical to SEQ ID NO:5. Preferably, the bacterial strain foruse in the invention has a 16s rRNA sequence that has the sequence ofSEQ ID NO:5.

In certain embodiments, the bacterial strain for use in the inventionhas a 16s rRNA sequence that is at least 97%, 98%, 99%, 99.5% or 99.9%identical to the 16s rRNA sequence of a bacterial strain of Blautiastercoris. Preferably, the bacterial strain for use in the invention hasa 16s rRNA sequence that is at least 97%, 98%, 99%, 99.5% or 99.9%identical to SEQ ID NO:1 or SEQ ID NO:3. Preferably, the sequenceidentity is to SEQ ID NO:3. Preferably, the bacterial strain for use inthe invention has the 16s rRNA sequence represented by SEQ ID NO:3. Incertain embodiments, the bacterial strain for use in the invention has a16s rRNA sequence that is at least 97%, 98%, 99%, 99.5% or 99.9%identical to the 16s rRNA sequence of a bacterial strain of Blautiawexlerae. Preferably, the bacterial strain for use in the invention hasa 16s rRNA sequence that is at least 97%, 98%, 99%, 99.5% or 99.9%identical to SEQ ID NO:2 or SEQ ID NO:4. Preferably, the sequenceidentity is to SEQ ID NO:4. Preferably, the bacterial strain for use inthe invention has the 16s rRNA sequence represented by SEQ ID NO:4.

Bacterial strains that are biotypes of the bacterium deposited underaccession number DSM 10507/14294 or biotypes of the bacteria depositedunder accession numbers NCIMB 42381 and NCIMB 42486 are also expected tobe effective for increasing the microbiota diversity and/or inducing thestability of the microbiota. A biotype is a closely related strain thathas the same or very similar physiological and biochemicalcharacteristics.

Strains that are biotypes of a bacterium deposited under accessionnumber DSM 10507/14294, NCIMB 42381 or NCIMB 42486 and that are suitablefor use in the invention may be identified by sequencing othernucleotide sequences for a bacterium deposited under accession numberDSM 10507/14294, NCIMB 42381 or NCIMB 42486. For example, substantiallythe whole genome may be sequenced and a biotype strain for use in theinvention may have at least 97%, 98%, 99%, 99.5% or 99.9% sequenceidentity across at least 80% of its whole genome (e.g. across at least85%, 90%, 95% or 99%, or across its whole genome). For example, in someembodiments, a biotype strain has at least 98% sequence identity acrossat least 98% of its genome or at least 99% sequence identity across 99%of its genome. Other suitable sequences for use in identifying biotypestrains may include hsp60 or repetitive sequences such as BOX, ERIC,(GTG)₅, or REP or [28]. Biotype strains may have sequences with at least97%, 98%, 99%, 99.5% or 99.9% sequence identity to the correspondingsequence of a bacterium deposited under accession number DSM10507/14294, NCIMB 42381 or NCIMB 42486. In some embodiments, a biotypestrain has a sequence with at least 97%, 98%, 99%, 99.5% or 99.9%sequence identity to the corresponding sequence of the Blautiahydrogenotrophica strain deposited under accession number DSM10507/14294 and comprises a 16S rRNA sequence that is at least 99%identical (e.g. at least 99.5% or at least 99.9% identical) to SEQ IDNO:5. In some embodiments, a biotype strain has a sequence with at least97%, 98%, 99%, 99.5% or 99.9% sequence identity to the correspondingsequence of the Blautia hydrogenotrophica strain deposited underaccession number DSM 10507/14294 and has the 16S rRNA sequence of SEQ IDNO:5.

Alternatively, strains that are biotypes of a bacterium deposited underaccession number DSM 10507/14294, NCIMB 42381 or NCIMB 42486 and thatare suitable for use in the invention may be identified by using theaccession number DSM 10507/14294 deposit, the accession number NCIMB42381 deposit, or the accession number NCIMB 42486 deposit, andrestriction fragment analysis and/or PCR analysis, for example by usingfluorescent amplified fragment length polymorphism (FAFLP) andrepetitive DNA element (rep)-PCR fingerprinting, or protein profiling,or partial 16S or 23s rDNA sequencing. In preferred embodiments, suchtechniques may be used to identify other Blautia hydrogenotrophica,Blautia stercoris or Blautia wexlerae strains.

In certain embodiments, strains that are biotypes of a bacteriumdeposited under accession number DSM 10507/14294, NCIMB 42381 or NCIMB42486 and that are suitable for use in the invention are strains thatprovide the same pattern as a bacterium deposited under accession numberDSM 10507/14294, NCIMB 42381 or NCIMB 42486 when analysed by amplifiedribosomal DNA restriction analysis (ARDRA), for example when usingSau3AI restriction enzyme (for exemplary methods and guidance see, forexample,[29]). Alternatively, biotype strains are identified as strainsthat have the same carbohydrate fermentation patterns as a bacteriumdeposited under accession number DSM 10507/14294, NCIMB 42381 or NCIMB42486.

Other Blautia strains that are useful in the compositions and methods ofthe invention, such as biotypes of a bacterium deposited under accessionnumber DSM 10507/14294, NCIMB 42381 or NCIMB 42486, may be identifiedusing any appropriate method or strategy, including the assays describedin the examples. For instance, strains for use in the invention may beidentified by culturing bacteria and administering to rats to test inthe distension assay. In particular, bacterial strains that have similargrowth patterns, metabolic type and/or surface antigens to a bacteriumdeposited under accession number DSM 10507/14294, NCIMB 42381 or NCIMB42486 may be useful in the invention. A useful strain will havecomparable microbiota modulatory activity to the DSM 10507/14294, NCIMB42381 or NCIMB 42486 strain. In particular, a biotype strain will elicitcomparable effects on the microbiota to the effects shown in theExamples, which may be identified by using the culturing andadministration protocols described in the Examples.

A particularly preferred strain of the invention is the Blautiahydrogenotrophica strain deposited under accession number DSM10507/14294. This is the exemplary BH strain tested in the examples andshown to be effective for increasing the microbiota diversity and/orinducing the stability of the microbiota. Therefore, the inventionprovides a cell, such as an isolated cell, of the Blautiahydrogenotrophica strain deposited under accession number DSM10507/14294, or a derivative thereof, for use in therapy, in particularfor the diseases and disorders described herein.

A derivative of the strain deposited under accession number DSM10507/14294, NCIMB 42381 or NCIMB 42486 may be a daughter strain(progeny) or a strain cultured (subcloned) from the original. Aderivative of a strain of the invention may be modified, for example atthe genetic level, without ablating the biological activity. Inparticular, a derivative strain of the invention is therapeuticallyactive. A derivative strain will have comparable microbiota modulatoryactivity to the original DSM 10507/14294, NCIMB 42381 or NCIMB 42486strain. In particular, a derivative strain will elicit comparableeffects on the microbiota to the effects shown in the Examples, whichmay be identified by using the culturing and administration protocolsdescribed in the Examples. A derivative of the DSM 10507/14294 strainwill generally be a biotype of the DSM 10507/14294 strain. A derivativeof the NCIMB 42381 strain will generally be a biotype of the NCIMB 42381strain. A derivative of the NCIMB 42486 strain will generally be abiotype of the NCIMB 42486 strain.

References to cells of the Blautia hydrogenotrophica strain depositedunder accession number DSM 10507/14294 encompass any cells that have thesame safety and therapeutic efficacy characteristics as the strainsdeposited under accession number DSM 10507/14294, and such cells areencompassed by the invention. References to cells of the Blautiastercoris strain deposited under accession number NCIMB 42381 encompassany cells that have the same safety and therapeutic efficacycharacteristics as the strains deposited under accession number NCIMB42381, and such cells are encompassed by the invention. References tocells of the Blautia wexlerae strain deposited under accession numberNCIMB 42486 encompass any cells that have the same safety andtherapeutic efficacy characteristics as the strains deposited underaccession number NCIMB 42486, and such cells are encompassed by theinvention.

In preferred embodiments, the bacterial strains in the compositions ofthe invention are viable and capable of partially or totally colonisingthe intestine.

Therapeutic Uses

In certain embodiments, the compositions of the invention are for use inincreasing the microbiota diversity and/or inducing the stability of themicrobiota. Reduced diversity of the microbiota and/or reduced stabilityof the microbiota are associated with numerous pathological diseases anddisorders, and the examples demonstrate that the compositions of theinvention may be effective for increasing the microbiota diversityand/or inducing the stability of the microbiota. Accordingly, thedisease or disorder to be treated or prevented using a composition ofthe invention is preferably a disease or disorder associated with alevel of microbiota diversity that is reduced relative to the microbiotadiversity of a healthy subject and/or a disease or disorder that isassociated with reduced stability of the microbiota. Thus, in someembodiments, the disease or disorder may be associated with a level ofmicrobiota diversity that is reduced relative to the microbiotadiversity of a healthy subject and also be associated with reducedstability of the microbiota.

In certain embodiments, the compositions of the invention are for use intreating or preventing a disease or disorder selected from IBS, IBD,obesity, type 2 diabetes, one or more infectious diseases, one or moreallergic diseases, one or more autoimmune diseases and one or moremetabolic diseases/disorders. Treatment or prevention of other diseasesand disorders is also envisaged. In certain embodiments, thecompositions of the invention are for use in treating or preventing IBSor IBD. In certain embodiments, the compositions of the invention arefor use in treating or preventing IBS. In certain embodiments, thecompositions of the invention are for use in treating or preventing IBD.In certain embodiments, the compositions of the invention are for use intreating or preventing one or more allergic diseases. In certainembodiments, the compositions of the invention are for use in treatingor preventing obesity. In certain embodiments, the compositions of theinvention are for use in treating or preventing one or more infectiousdiseases. In certain embodiments, the compositions of the invention arefor use in treating or preventing one or more autoimmune diseases. Incertain embodiments, the compositions of the invention are for use intreating or preventing one or more metabolic diseases/disorders.Preferably, the treatment or prevention comprises increasing themicrobiota diversity and/or inducing the stability of the microbiota inthe subject.

In certain embodiments, the one or more infectious diseases is selectedfrom a viral, bacterial or fungal disease. In certain embodiments, theone or more allergic diseases is asthma. In certain embodiments, the oneor more metabolic diseases/disorders is selected from diabetes, e.g.type 2 diabetes, and obesity. In certain embodiments, the one or moreautoimmune diseases is selected from multiple sclerosis and rheumatoidarthritis.

In certain embodiments, the compositions of the invention are for use intreating or preventing IBS, IBD, obesity, type 2 diabetes, one of moreinfectious diseases, one or more allergic diseases, one or moreautoimmune diseases or one or more metabolic diseases/disorders byincreasing the microbiota diversity in the microbiota. In certainembodiments, the compositions of the invention are for use in treatingor preventing IBS or IBD by inducing the stability of the microbiota. Incertain embodiments, the compositions of the invention are for use intreating or preventing IBS by inducing the stability of the microbiota

In preferred embodiments, the invention provides a compositioncomprising a bacterial strain of the genus Blautia, for use in thetreatment or prevention of IBD, IBS, obesity, type 2 diabetes, one ormore infectious diseases, one or more allergic diseases, one or moreautoimmune diseases or one or more metabolic diseases/disorders, whereinthe treatment or prevention comprises increasing the microbiotadiversity and/or inducing the stability of the microbiota in thesubject.

In some embodiments, the invention provides a composition comprising abacterial strain of the genus Blautia for use in treating or preventinga disease or disorder selected from IBS, IBD, obesity, type 2 diabetes,one or more infectious diseases, one or more allergic diseases, one ormore autoimmune diseases and one or more metabolic diseases/disorders.In some embodiments, the invention provides a method of treating orpreventing a disease or disorder selected from IBS, IBD, obesity, type 2diabetes, one or more infectious diseases, one or more allergicdiseases, one or more autoimmune diseases and one or more metabolicdiseases/disorders, comprising administering a composition comprising abacterial strain of the genus Blautia.

In preferred embodiments, the compositions of the invention comprise thebacterium deposited under accession number DSM 10507/14294 and are foruse in increasing the microbiota diversity and/or inducing the stabilityof the microbiota in the subject in the treatment of IBD, IBS, obesity,type 2 diabetes, one or more infectious diseases, one or more allergicdiseases, one or more autoimmune diseases or one or more metabolicdiseases/disorders. In further preferred embodiments, the compositionsof the invention comprise the bacterium deposited under accession numberDSM 10507/14294 and are for use in treating or preventing IBD, IBS,obesity, type 2 diabetes, one or more infectious diseases, one or moreallergic diseases, one or more autoimmune diseases or one or moremetabolic diseases/disorders by increasing the microbiota diversityand/or inducing the stability of the microbiota.

In some embodiments, the pathogenesis of the disease or disorder affectsthe intestine. In some embodiments, the pathogenesis of the disease ordisorder does not affect the intestine. In some embodiments, thepathogenesis of the disease or disorder is not localised at theintestine. In some embodiments, the treating or preventing occurs at asite other than at the intestine. In some embodiments, the treating orpreventing occurs at the intestine and also at a site other than at theintestine. In certain embodiments, the disease or disorder is systemic.

In certain embodiments, the compositions are for use in subjects thatexhibit, or are expected to exhibit, reduced levels of microbiotadiversity, for example, when compared to a healthy subject, or apopulation of healthy subjects. For example, in some embodiments, thecomposition is for use in treating a subject having less than 101different bacterial species (e.g. less than 100, 99, 98, 97, 96, 95, 93,90, 85, 80, 75 or 70 bacterial species) and/or less than 195 differentstrains (e.g. less than 193, 190, 187, 185, 183, 180, 175, 170, 165,160, 150, 140 bacterial strains) in its microbiota. For example, in someembodiments, the composition is for use in treating a subject that hasat least one bacterial genus (e.g. at least 2, 3, 4, 5, 6, 7, 8, 9 or 10bacterial genera) fewer in its intestinal microbiota compared to ahealthy subject or compared to a population of healthy subjects. In someembodiments, the treatment or prevention comprises a step of diagnosinga subject as having a reduced level of microbiota diversity and then ifa reduced level of diversity is found to be present, the subject is thentreated with a composition according to the invention.

In certain embodiments, the compositions are for use in subjects thatexhibit, or are expected to exhibit, reduced stability of themicrobiota. In some embodiments, the compositions are for use insubjects that exhibit, or are expected to exhibit, reduced stability inits microbiota, for example, when compared to a healthy subject, or apopulation of healthy subjects. In some embodiments, the treatment orprevention comprises a step of diagnosing a subject as having a reducedstability in its microbiota and then if reduced stability is found to bepresent, the subject is then treated with a composition according to theinvention.

In certain embodiments, the subject is an infant. In certainembodiments, the subject is a child.

In certain embodiments, the subject is an adult.

In certain embodiments, the subject is a healthy subject. For example,in some embodiments in which the composition is used for preventing adisease or disorder, the subject is a healthy subject, optionally oneidentified as being at risk of developing a disease or disordercharacterised by a reduction in microbiota diversity.

In certain embodiments, the subject has previously received, isreceiving, or will be receiving antibiotic treatment. Accordingly, insome embodiments, the treatment or prevention comprises administeringthe composition of the invention after, together with, or beforeantibiotic treatment. The composition of the invention and the one ormore antibiotics may be for separate, simultaneous or sequentialadministration.

In some embodiments, the composition of the invention is for use in amethod of increasing the microbiota diversity and/or inducing thestability of the microbiota in a subject having an increased level ofhydrogen in their breath relative to a healthy subject. In someembodiments, the composition of the invention is for use in reducing thehydrogen level in the breath of a subject exhibiting or who is expectedto exhibit a reduced level of diversity of its microbiota and/or reducedstability of the microbiota. The subject is preferably a subjectdiagnosed as having IBS, IBD, obesity, type 2 diabetes, one or moreinfectious diseases, one or more allergic diseases, one or moreautoimmune diseases and/or one or more metabolic diseases/disorders.Treatment with a composition of the invention reduces the level ofhydrogen detected in hydrogen breath tests. Accordingly, the hydrogenlevels are preferably assessed using a hydrogen breath test. Thehydrogen breath test is well known in the art and so the skilled personwill know how to conduct such a test. In some embodiments, the subjectis administered lactulose as the substrate for the test.

The hydrogen breath test is also a useful tool for monitoring theeffectiveness or likely effectiveness of increasing the microbiotadiversity and/or inducing the stability of the microbiota and oftreatment or prevention using a composition of the invention. Forexample, a reduction in the level of hydrogen detected in a subject'sbreath following treatment with a composition of the invention mayindicate that the treatment is having an increasing, stabilising,therapeutic or preventative effect. Accordingly, in some embodiments themethods and uses of the invention further comprise monitoring thehydrogen level in a subject's breath during and/or following treatmentwith a composition of the invention and thereby assessing theeffectiveness or likely effectiveness of increasing, stabilising,treatment or prevention. For example, hydrogen levels may be monitoredat one or more (e.g. 1, 2, 3, 4 or more than 4) times, for example,including before treatment, at the start of treatment, during treatment,at the end of treatment and/or following treatment, as desired. In someembodiments, the level of hydrogen in the subject's breath at the endand/or following the dosing period (during which the composition isadministered to the subject) is compared to the level at the startand/or before the dosing period and a reduction in the level indicatesthe effectiveness or likely effectiveness of the increasing,stabilising, treatment or prevention. For example, in embodiments inwhich the dosing period is 16 days, it may be desirable to takemeasurements at day 1 and day 16, or for example at day 1, day 2, day 15and day 16. In some embodiments, multiple measurements are taken and themean of those measurements obtained (for example, the mean of day 1 andday 2 and the mean of day 15 and day 16). In some embodiments, areduction in at least 40 ppm in the hydrogen level Cmax indicates thatthe increasing, stabilising, treatment or prevention is effective orlikely to be effective. In some embodiments, the hydrogen level in thesubject's breath is measured only once, for example, at the end of orfollowing treatment, and the finding that the level is at or close to apredetermined level is indicative that the increasing stabilising,treatment or prevention is likely to have been effective. The hydrogenbreath test is a standard assay and so predetermined levels are known inthe art.

Treatment or prevention may refer to, for example, an alleviation of theseverity of symptoms or a reduction in the frequency of exacerbations orthe range of triggers that are a problem for the subject.

Bacteria in the microbiota may be detected in faeces from a subject,using standard techniques, such as the qPCR techniques used in theexamples.

Modes of administration Preferably, the compositions of the inventionare to be administered to the gastrointestinal tract in order to enabledelivery to and/or partial or total colonisation of the intestine withthe bacterial strain of the invention. Generally, the compositions ofthe invention are administered orally, but they may be administeredrectally, intranasally, or via buccal or sublingual routes.

In certain embodiments, the compositions of the invention may beadministered as a foam, as a spray or a gel.

In certain embodiments, the compositions of the invention may beadministered as a suppository, such as a rectal suppository, for examplein the form of a theobroma oil (cocoa butter), synthetic hard fat (e.g.suppocire, witepsol), glycero-gelatin, polyethylene glycol, or soapglycerin composition.

In certain embodiments, the composition of the invention is administeredto the gastrointestinal tract via a tube, such as a nasogastric tube,orogastric tube, gastric tube, jejunostomy tube (J tube), percutaneousendoscopic gastrostomy (PEG), or a port, such as a chest wall port thatprovides access to the stomach, jejunum and other suitable access ports.

The compositions of the invention may be administered once, or they maybe administered sequentially as part of a treatment regimen. In certainembodiments, the compositions of the invention are to be administereddaily. The examples demonstrate that daily administration providessuccessful delivery and clinical benefits.

In certain embodiments, the compositions of the invention areadministered regularly, such as daily, every two days, or weekly, for anextended period of time, such as for at least one week, two weeks, onemonth, two months, six months, or one year. The examples demonstratethat B. hydrogenotrophica administration may not result in permanentcolonisation of the intestines, so regular administration for extendedperiods of time may provide greater therapeutic and/or prophylacticbenefits.

In certain embodiments of the invention, treatment according to theinvention is accompanied by assessment of the subject's gut microbiota.Treatment may be repeated if delivery of and/or partial or totalcolonisation with the strain of the invention is not achieved such thatefficacy is not observed, or treatment may be ceased if delivery and/orpartial or total colonisation is successful and efficacy is observed.

In certain embodiments, the composition of the invention may beadministered to a pregnant animal, for example a mammal such as a humanin order to prevent reduced levels of diversity in the microbiota and/orreduced stability of the microbiota developing in her child in uteroand/or after it is born.

The compositions of the invention may be administered to a subject thathas been diagnosed with reduced microbiota diversity relative to ahealthy subject and/or reduced stability of the microbiota or a diseaseor disorder associated with reduced microbiota diversity relative to ahealthy subject and/or reduced stability of the microbiota, or that hasbeen identified as being at risk of reduced microbiota diversityrelative to a healthy subject and/or reduced stability of themicrobiota. The compositions may also be administered as a prophylacticmeasure to prevent the development of reduced microbiota diversityrelative to a healthy subject and/or reduced stability of the microbiotain a healthy subject.

The compositions of the invention may be administered to a subject thathas been identified as having an abnormal gut microbiota. For example,the subject may have reduced or absent colonisation by Blautia, and inparticular Blautia hydrogenotrophica, Blautia stercoris or Blautiawexlerae.

The compositions of the invention may be administered as a food product,such as a nutritional supplement.

Generally, the compositions of the invention are for the treatment ofhumans, although they may be used to treat animals including monogastricmammals such as poultry, pigs, cats, dogs, horses or rabbits. Thecompositions of the invention may be useful for enhancing the growth andperformance of animals. If administered to animals, oral gavage may beused.

Compositions Generally, the composition of the invention comprisesbacteria. In preferred embodiments of the invention, the composition isformulated in freeze-dried form. For example, the composition of theinvention may comprise granules or gelatin capsules, for example hardgelatin capsules, comprising a bacterial strain of the invention.

Preferably, the composition of the invention comprises lyophilisedbacteria. Lyophilisation of bacteria is a well-established procedure andrelevant guidance is available in, for example, references [30-32]. Theexamples demonstrate that lyophilisate compositions are particularlyeffective.

Alternatively, the composition of the invention may comprise a live,active bacterial culture.

In some embodiments, the bacterial strain in the composition of theinvention has not been inactivated, for example, has not beenheat-inactivated. In some embodiments, the bacterial strain in thecomposition of the invention has not been killed, for example, has notbeen heat-killed. In some embodiments, the bacterial strain in thecomposition of the invention has not been attenuated, for example, hasnot been heat-attenuated. For example, in some embodiments, thebacterial strain in the composition of the invention has not beenkilled, inactivated and/or attenuated. For example, in some embodiments,the bacterial strain in the composition of the invention is live. Forexample, in some embodiments, the bacterial strain in the composition ofthe invention is viable. For example, in some embodiments, the bacterialstrain in the composition of the invention is capable of partially ortotally colonising the intestine. For example, in some embodiments, thebacterial strain in the composition of the invention is viable andcapable of partially or totally colonising the intestine.

In some embodiments, the composition comprises a mixture of livebacterial strains and bacterial strains that have been killed.

In preferred embodiments, the composition of the invention isencapsulated to enable delivery of the bacterial strain to theintestine. Encapsulation protects the composition from degradation untildelivery at the target location through, for example, rupturing withchemical or physical stimuli such as pressure, enzymatic activity, orphysical disintegration, which may be triggered by changes in pH. Anyappropriate encapsulation method may be used. Exemplary encapsulationtechniques include entrapment within a porous matrix, attachment oradsorption on solid carrier surfaces, self-aggregation by flocculationor with cross-linking agents, and mechanical containment behind amicroporous membrane or a microcapsule. Guidance on encapsulation thatmay be useful for preparing compositions of the invention is availablein, for example, references [33] and [34].

The composition may be administered orally and may be in the form of atablet, capsule or powder. Encapsulated products are preferred becauseBlautia are anaerobes. Other ingredients (such as vitamin C, forexample), may be included as oxygen scavengers and prebiotic substratesto improve the delivery and/or partial or total colonisation andsurvival in vivo. Alternatively, the probiotic composition of theinvention may be administered orally as a food or nutritional product,such as milk or whey based fermented dairy product, or as apharmaceutical product.

The composition may be formulated as a probiotic.

A composition of the invention includes a therapeutically effectiveamount of a bacterial strain of the invention. A therapeuticallyeffective amount of a bacterial strain is sufficient to exert abeneficial effect upon a subject. A therapeutically effective amount ofa bacterial strain may be sufficient to result in delivery to and/orpartial or total colonisation of the subject's intestine.

A suitable daily dose of the bacteria, for example for an adult human,may be from about 1×10³ to about 1×10¹¹ colony forming units (CFU); forexample, from about 1×10⁷ to about 1×10¹⁰ CFU; in another example fromabout 1×10⁷ to about 1×10¹¹ CFU; in another example from about 1×10⁸ toabout 1×10¹⁰ CFU; in another example from about 1×10⁸ to about 1×10¹¹CFU; in another example from about 1×10⁶ to about 1×10¹⁰ CFU.

In certain embodiments, the dose of the bacteria is at least 10⁹ cellsper day, such as at least 10¹⁰, at least 10¹¹, or at least 10¹² cellsper day.

In certain embodiments, the composition contains the bacterial strain inan amount of from about 1×10⁶ to about 1×10¹¹ CFU/g, respect to theweight of the composition; for example, from about 1×10⁸ to about 1×10¹⁰CFU/g. The dose may be, for example, 1 g, 3 g, 5 g, and 10 g.

Typically, a probiotic, such as the composition of the invention, isoptionally combined with at least one suitable prebiotic compound. Aprebiotic compound is usually a non-digestible carbohydrate such as anoligo- or polysaccharide, or a sugar alcohol, which is not degraded orabsorbed in the upper digestive tract. Known prebiotics includecommercial products such as inulin and transgalacto-oligosaccharides.

In certain embodiments, the probiotic composition of the presentinvention includes a prebiotic compound in an amount of from about 1 toabout 30% by weight, respect to the total weight composition, (e.g. from5 to 20% by weight). Carbohydrates may be selected from the groupconsisting of: fructo-oligosaccharides (or FOS), short-chainfructo-oligosaccharides, inulin, isomalt-oligosaccharides, pectins,xylo-oligosaccharides (or XOS), chitosan-oligosaccharides (or COS),beta-glucans, arable gum modified and resistant starches, polydextrose,D-tagatose, acacia fibers, carob, oats, and citrus fibers. In oneaspect, the prebiotics are the short-chain fructo-oligosaccharides (forsimplicity shown herein below as FOSs-c.c); said FOSs-c.c. are notdigestible carbohydrates, generally obtained by the conversion of thebeet sugar and including a saccharose molecule to which three glucosemolecules are bonded.

The compositions of the invention may comprise pharmaceuticallyacceptable excipients or carriers. Examples of such suitable excipientsmay be found in the reference [35]. Acceptable carriers or diluents fortherapeutic use are well known in the pharmaceutical art and aredescribed, for example, in reference [36]. Examples of suitable carriersinclude lactose, starch, glucose, methyl cellulose, magnesium stearate,mannitol, sorbitol and the like. Examples of suitable diluents includeethanol, glycerol and water. The choice of pharmaceutical carrier,excipient or diluent can be selected with regard to the intended routeof administration and standard pharmaceutical practice. Thepharmaceutical compositions may comprise as, or in addition to, thecarrier, excipient or diluent any suitable binder(s), lubricant(s),suspending agent(s), coating agent(s), solubilising agent(s). Examplesof suitable binders include starch, gelatin, natural sugars such asglucose, anhydrous lactose, free-flow lactose, beta-lactose, cornsweeteners, natural and synthetic gums, such as acacia, tragacanth orsodium alginate, carboxymethyl cellulose and polyethylene glycol.Examples of suitable lubricants include sodium oleate, sodium stearate,magnesium stearate, sodium benzoate, sodium acetate, sodium chloride andthe like. Preservatives, stabilizers, dyes and even flavouring agentsmay be provided in the pharmaceutical composition. Examples ofpreservatives include sodium benzoate, sorbic acid, cysteine and estersof p-hydroxybenzoic acid. Antioxidants and suspending agents may be alsoused. A further example of a suitable carrier is saccharose. A furtherexample of a preservative is cysteine.

The compositions of the invention may be formulated as a food product.For example, a food product may provide nutritional benefit in additionto the therapeutic effect of the invention, such as in a nutritionalsupplement. Similarly, a food product may be formulated to enhance thetaste of the composition of the invention or to make the compositionmore attractive to consume by being more similar to a common food item,rather than to a pharmaceutical composition. In certain embodiments, thecomposition of the invention is formulated as a milk-based product. Theterm “milk-based product” means any liquid or semi-solid milk- orwhey-based product having a varying fat content. The milk-based productcan be, e.g., cow's milk, goat's milk, sheep's milk, skimmed milk, wholemilk, milk recombined from powdered milk and whey without anyprocessing, or a processed product, such as yoghurt, curdled milk, curd,sour milk, sour whole milk, butter milk and other sour milk products.Another important group includes milk beverages, such as whey beverages,fermented milks, condensed milks, infant or baby milks; flavoured milks,ice cream; milk-containing food such as sweets.

In certain embodiments, the compositions of the invention contain asingle bacterial strain or species and do not contain any otherbacterial strains or species. Such compositions may comprise only deminimis or biologically irrelevant amounts of other bacterial strains orspecies. Such compositions may be a culture or lyophilisate that issubstantially free from other species of organism.

In certain embodiments, the compositions of the invention comprise oneor more bacterial strains of the genus Blautia, for example, a Blautiahydrogenotrophica, and do not contain any other bacterial genus, orwhich comprise only de minimis or biologically irrelevant amounts ofbacteria from another genus. In certain embodiments, the compositions ofthe invention comprise a single species of Blautia, for example, aBlautia hydrogenotrophica, and do not contain any other bacterialspecies, or which comprise only de minimis or biologically irrelevantamounts of bacteria from another species. In certain embodiments, thecompositions of the invention comprise a single strain of Blautia, forexample, of Blautia hydrogenotrophica, and do not contain any otherbacterial strains or species, or which comprise only de minimis orbiologically irrelevant amounts of bacteria from another strain orspecies.

In some embodiments, the compositions of the invention comprise morethan one bacterial strain or species. For example, in some embodiments,the compositions of the invention comprise more than one strain fromwithin the same species (e.g. more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,15, 20, 25, 30, 35, 40 or 45 strains), and, optionally, do not containbacteria from any other species. In some embodiments, the compositionsof the invention comprise less than 50 strains from within the samespecies (e.g. less than 45, 40, 35, 30, 25, 20, 15, 12, 10, 9, 8, 7, 6,5, 4 or 3 strains), and, optionally, do not contain bacteria from anyother species. In some embodiments, the compositions of the inventioncomprise 1-40, 1-30, 1-20, 1-19, 1-18, 1-15, 1-10, 1-9, 1-8, 1-7, 1-6,1-5, 1-4, 1-3, 1-2, 2-50, 2-40, 2-30, 2-20, 2-15, 2-10, 2-5, 6-30, 6-15,16-25, or 31-50 strains from within the same species and, optionally, donot contain bacteria from any other species. In some embodiments, thecompositions of the invention comprise more than one species from withinthe same genus (e.g. more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15,17, 20, 23, 25, 30, 35 or 40 species), and, optionally, do not containbacteria from any other genus. In some embodiments, the compositions ofthe invention comprise less than 50 species from within the same genus(e.g. less than 50, 45, 40, 35, 30, 25, 20, 15, 12, 10, 8, 7, 6, 5, 4 or3 species), and, optionally, do not contain bacteria from any othergenus. In some embodiments, the compositions of the invention comprise1-50, 1-40, 1-30, 1-20, 1-15, 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3,1-2, 2-50, 2-40, 2-30, 2-20, 2-15, 2-10, 2-5, 6-30, 6-15, 16-25, or31-50 species from within the same genus and, optionally, do not containbacteria from any other genus. The invention comprises any combinationof the foregoing.

In some embodiments, the composition comprises a microbial consortium.For example, in some embodiments, the composition comprises the Blautiabacterial strain, for example, a Blautia hydrogenotrophica bacterialstrain as part of a microbial consortium. For example, in someembodiments, the Blautia bacterial strain is present in combination withone or more (e.g. at least 2, 3, 4, 5, 10, 15 or 20) other bacterialstrains from other genera with which it can live symbiotically in vivoin the intestine. For example, in some embodiments, the compositioncomprises a bacterial strain of Blautia hydrogenotrophica in combinationwith a bacterial strain from a different genus. In some embodiments, themicrobial consortium comprises two or more bacterial strains obtainedfrom a faeces sample of a single organism, e.g. a human. In someembodiments, the microbial consortium is not found together in nature.For example, in some embodiments, the microbial consortium comprisesbacterial strains obtained from faeces samples of at least two differentorganisms. In some embodiments, the two different organisms are from thesame species, e.g. two different humans. In some embodiments, the twodifferent organisms are an infant human and an adult human. In someembodiments, the two different organisms are a human and a non-humanmammal.

In some embodiments, the composition of the invention additionallycomprises a bacterial strain that has the same safety and therapeuticefficacy characteristics as the Blautia hydrogenotrophica straindeposited under accession number DSM 10507/14294, but which is not theBlautia hydrogenotrophica strain deposited under accession number DSM10507/14294, or which is not a Blautia hydrogenotrophica or which is nota Blautia.

In some embodiments in which the composition of the invention comprisesmore than one bacterial strain, species or genus, the individualbacterial strains, species or genera may be for separate, simultaneousor sequential administration. For example, the composition may compriseall of the more than one bacterial strain, species or genera, or thebacterial strains, species or genera may be stored separately and beadministered separately, simultaneously or sequentially.

In some embodiments, the more than one bacterial strains, species orgenera are stored separately but are mixed together prior to use.

In some embodiments, the bacterial strain for use in the invention isobtained from human adult faeces. In some embodiments in which thecomposition of the invention comprises more than one bacterial strain,all of the bacterial strains are obtained from human adult faeces or ifother bacterial strains are present they are present only in de minimisamounts. In some embodiments, the bacteria may have been culturedsubsequent to being obtained from the human adult faeces and being usedin a composition of the invention.

In some embodiments, the one or more Blautia bacterial strains is/arethe only therapeutically active agent(s) in a composition of theinvention. In some embodiments, the bacterial strain(s) in thecomposition is/are the only therapeutically active agent(s) in acomposition of the invention.

The compositions for use in accordance with the invention may or may notrequire marketing approval.

In certain embodiments, the invention provides the above pharmaceuticalcomposition, wherein said bacterial strain is lyophilised. In certainembodiments, the invention provides the above pharmaceuticalcomposition, wherein said bacterial strain is spray dried. In certainembodiments, the invention provides the above pharmaceuticalcomposition, wherein the bacterial strain is lyophilised or spray driedand wherein it is live. In certain embodiments, the invention providesthe above pharmaceutical composition, wherein the bacterial strain islyophilised or spray dried and wherein it is viable. In certainembodiments, the invention provides the above pharmaceuticalcomposition, wherein the bacterial strain is lyophilised or spray driedand wherein it is capable of partially or totally colonising theintestine. In certain embodiments, the invention provides the abovepharmaceutical composition, wherein the bacterial strain is lyophilisedor spray dried and wherein it is viable and capable of partially ortotally colonising the intestine.

In some cases, the lyophilised or spray dried bacterial strain isreconstituted prior to administration. In some cases, the reconstitutionis by use of a diluent described herein.

The compositions of the invention can comprise pharmaceuticallyacceptable excipients, diluents or carriers.

In certain embodiments, the invention provides a pharmaceuticalcomposition comprising: a bacterial strain as used in the invention; anda pharmaceutically acceptable excipient, carrier or diluent; wherein thebacterial strain is in an amount sufficient to increase the microbiotadiversity in a subject and/or induce stability of the microbiota and/ortreat a disorder associated with reduced microbiota diversity and/orreduced stability of the microbiota when administered to a subject inneed thereof, microbiota diversity, for example, a disease or disordersuch as IBS, IBD, obesity, type 2 diabetes, one or more infectiousdiseases, one or more allergic diseases, one or more autoimmune diseasesor one or more metabolic diseases/disorders.

In certain embodiments, the invention provides the above pharmaceuticalcomposition, wherein the amount of the bacterial strain is from about1×10³ to about 1×10¹¹ colony forming units per gram with respect to aweight of the composition.

In certain embodiments, the invention provides the above pharmaceuticalcomposition, wherein the composition is administered at a dose of 1 g, 3g, 5 g or 10 g.

In certain embodiments, the invention provides the above pharmaceuticalcomposition, wherein the composition is administered by a methodselected from the group consisting of oral, rectal, subcutaneous, nasal,buccal, and sublingual.

In certain embodiments, the invention provides the above pharmaceuticalcomposition, comprising a carrier selected from the group consisting oflactose, starch, glucose, methyl cellulose, magnesium stearate, mannitoland sorbitol.

In certain embodiments, the invention provides the above pharmaceuticalcomposition, comprising a diluent selected from the group consisting ofethanol, glycerol and water.

In certain embodiments, the invention provides the above pharmaceuticalcomposition, comprising an excipient selected from the group consistingof starch, gelatin, glucose, anhydrous lactose, free-flow lactose,beta-lactose, corn sweetener, acacia, tragacanth, sodium alginate,carboxymethyl cellulose, polyethylene glycol, sodium oleate, sodiumstearate, magnesium stearate, sodium benzoate, sodium acetate and sodiumchloride.

In certain embodiments, the invention provides the above pharmaceuticalcomposition, further comprising at least one of a preservative, anantioxidant and a stabilizer.

In certain embodiments, the invention provides the above pharmaceuticalcomposition, comprising a preservative selected from the groupconsisting of sodium benzoate, sorbic acid and esters ofp-hydroxybenzoic acid.

In certain embodiments, the invention provides the above pharmaceuticalcomposition, wherein said bacterial strain is lyophilised.

In certain embodiments, the invention provides the above pharmaceuticalcomposition, wherein when the composition is stored in a sealedcontainer at about 4° C. or about 25° C. and the container is placed inan atmosphere having 50% relative humidity, at least 80% of thebacterial strain as measured in colony forming units, remains after aperiod of at least about: 1 month, 3 months, 6 months, 1 year, 1.5years, 2 years, 2.5 years or 3 years.

In some embodiments, the composition of the invention is provided in asealed container comprising a composition as described herein. In someembodiments, the sealed container is a sachet or bottle. In someembodiments, the composition of the invention is provided in a syringecomprising a composition as described herein.

The composition of the present invention may, in some embodiments, beprovided as a pharmaceutical formulation. For example, the compositionmay be provided as a tablet or capsule. In some embodiments, the capsuleis a gelatine capsule (“gel-cap”).

In some embodiments, the compositions of the invention are administeredorally. Oral administration may involve swallowing, so that the compoundenters the gastrointestinal tract, and/or buccal, lingual, or sublingualadministration by which the compound enters the blood stream directlyfrom the mouth.

Pharmaceutical formulations suitable for oral administration includesolid plugs, solid microparticulates, semi-solid and liquid (includingmultiple phases or dispersed systems) such as tablets; soft or hardcapsules containing multi- or nano-particulates, liquids (e.g. aqueoussolutions), emulsions or powders; lozenges (including liquid-filled);chews; gels; fast dispersing dosage forms; films; ovules; sprays; andbuccal/mucoadhesive patches.

In some embodiments the pharmaceutical formulation is an entericformulation, i.e. a gastro-resistant formulation (for example, resistantto gastric pH) that is suitable for delivery of the composition of theinvention to the intestine by oral administration. Enteric formulationsmay be particularly useful when the bacteria or another component of thecomposition is acid-sensitive, e.g. prone to degradation under gastricconditions.

In some embodiments, the enteric formulation comprises an entericcoating. In some embodiments, the formulation is an enteric-coateddosage form. For example, the formulation may be an enteric-coatedtablet or an enteric-coated capsule, or the like. The enteric coatingmay be a conventional enteric coating, for example, a conventionalcoating for a tablet, capsule, or the like for oral delivery. Theformulation may comprise a film coating, for example, a thin film layerof an enteric polymer, e.g. an acid-insoluble polymer.

In some embodiments, the enteric formulation is intrinsically enteric,for example, gastro-resistant without the need for an enteric coating.Thus, in some embodiments, the formulation is an enteric formulationthat does not comprise an enteric coating. In some embodiments, theformulation is a capsule made from a thermogelling material. In someembodiments, the thermogelling material is a cellulosic material, suchas methylcellulose, hydroxymethylcellulose orhydroxypropylmethylcellulose (HPMC). In some embodiments, the capsulecomprises a shell that does not contain any film forming polymer. Insome embodiments, the capsule comprises a shell and the shell compriseshydroxypropylmethylcellulose and does not comprise any film formingpolymer (e.g. see [37]). In some embodiments, the formulation is anintrinsically enteric capsule (for example, Vcaps® from Capsugel).

In some embodiments, the formulation is a soft capsule. Soft capsulesare capsules which may, owing to additions of softeners, such as, forexample, glycerol, sorbitol, maltitol and polyethylene glycols, presentin the capsule shell, have a certain elasticity and softness. Softcapsules can be produced, for example, on the basis of gelatine orstarch. Gelatine-based soft capsules are commercially available fromvarious suppliers. Depending on the method of administration, such as,for example, orally or rectally, soft capsules can have various shapes,they can be, for example, round, oval, oblong or torpedo-shaped. Softcapsules can be produced by conventional processes, such as, forexample, by the Scherer process, the Accogel process or the droplet orblowing process.

Culturing Methods

The bacterial strains for use in the present invention can be culturedusing standard microbiology techniques as detailed in, for example,references [38-40].

The solid or liquid medium used for culture may be YCFA agar or YCFAmedium. YCFA medium may include (per 100 ml, approximate values):Casitone (1.0 g), yeast extract (0.25 g), NaHCO₃ (0.4 g), cysteine (0.1g), K₂HPO₄ (0.045 g), KH₂PO₄ (0.045 g), NaCl (0.09 g), (NH₄)₂SO₄ (0.09g), MgSO₄.7H₂O (0.009 g), CaCl₂ (0.009 g), resazurin (0.1 mg), hemin (1mg), biotin (1 μg), cobalamin (1 μg), p-aminobenzoic acid (3 μg), folicacid (5 μg), and pyridoxamine (15 μg).

Bacterial Strains for Use in Vaccine Compositions

The inventors have identified that the bacterial strains of theinvention are useful for treating or preventing diseases or disordersassociated with a level of microbiota diversity that is reduced relativeto the microbiota diversity of a healthy subject (or relative to themicrobiota diversity of a population of healthy subjects) and/ordiseases or disorders that are associated with reduced stability of themicrobiota compared to a healthy subject (or compared to a population ofhealthy subjects). This is likely to be a result of the effect that thebacterial strains of the invention have on the host immune system.Therefore, the compositions of the invention may also be useful forpreventing such diseases or disorders when administered as vaccinecompositions. In certain such embodiments, the bacterial strains of theinvention are viable. In certain such embodiments, the bacterial strainsof the invention are capable of partially or totally colonising theintestine. In certain such embodiments, the bacterial strains of theinvention are viable and capable of partially or totally colonising theintestine. In other certain such embodiments, the bacterial strains ofthe invention may be killed, inactivated or attenuated. In certain suchembodiments, the compositions may comprise a vaccine adjuvant. Incertain embodiments, the compositions are for administration viainjection, such as via subcutaneous injection.

General

The practice of the present invention will employ, unless otherwiseindicated, conventional methods of chemistry, biochemistry, molecularbiology, immunology and pharmacology, within the skill of the art. Suchtechniques are explained fully in the literature. See, e.g., references[41] and [42-48], etc.

The term “comprising” encompasses “including” as well as “consisting”e.g. a composition “comprising” X may consist exclusively of X or mayinclude something additional e.g. X+Y.

The term “about” in relation to a numerical value x is optional andmeans, for example, x±10%.

The word “substantially” does not exclude “completely” e.g. acomposition which is “substantially free” from Y may be completely freefrom Y. Where necessary, the word “substantially” may be omitted fromthe definition of the invention.

References to a percentage sequence identity between two nucleotidesequences means that, when aligned, that percentage of nucleotides arethe same in comparing the two sequences. This alignment and the percenthomology or sequence identity can be determined using software programsknown in the art, for example those described in section 7.7.18 of ref[49]. A preferred alignment is determined by the Smith-Waterman homologysearch algorithm using an affine gap search with a gap open penalty of12 and a gap extension penalty of 2, BLOSUM matrix of 62. TheSmith-Waterman homology search algorithm is disclosed in ref [50].

Unless specifically stated, a process or method comprising numeroussteps may comprise additional steps at the beginning or end of themethod, or may comprise additional intervening steps. Also, steps may becombined, omitted or performed in an alternative order, if appropriate.

Various embodiments of the invention are described herein. It will beappreciated that the features specified in each embodiment may becombined with other specified features, to provide further embodiments.In particular, embodiments highlighted herein as being suitable, typicalor preferred may be combined with each other (except when they aremutually exclusive).

MODES FOR CARRYING OUT THE INVENTION Example 1—Changes in PatientMicrobiota after Blautia hydrogenotrophica Treatment

Summary

The effect of Blautia hydrogenotrophica on the diversity and stabilityof patient microbiota was tested in healthy and IBS patients.

Methodology

Study Design

A Phase I clinical trial was conducted in which Blautiahydrogenotrophica (“Blautix”, strain deposited under accession numberDSM 10507 and also under accession number DSM 14294) was administered tohuman patients having IBS or healthy human patients. Patients wereadministered Blautix during a dosing period (days 1-16) with the washoutperiod being day 19-23. Faecal samples were collected from IBS & healthysubjects, placebo or Blautix treated, at: baseline, day 1 (D1) prior totreatment; end of treatment day 16 (D-16); and at end of study (EOS),which was 2-4 weeks (wash-out) post-treatment.

16S Amplicon Sequencing

A Qiagen DNeasy Blood & Tissue Kit was used following the manufacturer'sinstructions, to extract microbial DNA from 0.2 g of frozen faecalsamples from IBS & Healthy subjects, placebo or Blautix treated, at:baseline, day 1 (D1) prior to treatment; end of treatment day 16 (D-16);and at end of study (EOS), which was 2-4 weeks (wash-out)post-treatment.

Preparation and sequencing of the 16S rRNA gene amplicons was carriedout using the 16S Sequencing Library Preparation Nextera protocoldeveloped by Illumina (San Diego, Calif., USA). 50 ng of each of the DNAfaecal extracts was amplified using PCR and primers targeting the V3/V4variable region of the 16S rRNA gene. The products were purified andforward and reverse barcodes were attached by a second round of adapterPCR. The resulting PCR products were purified, quantified and equimolaramounts of each amplicon were then pooled before being sent forsequencing to the commercial Supplier GATC Gmbh, on either the MiSeq(2×250 bp chemistry) or HiSeq (2×300 bp chemistry) platforms.

Data Analysis (Post-Sequencing)

The raw sequence data was merge trimmed using flash methodology. Thisfilters out low quality reads. The USEARCH pipeline methodology (version8.1.1861_i86 Jinux64) was used to identify singletons and hide them fromthe OTU (Operational Taxonomic Unit) generating step. The UPARSEalgorithm was used to cluster the sequences into OTUs. Chimericsequences generated in the amplification step were removed using theUCHIME chimera removal algorithm with the Chimeraslayer referencedatabase (downloaded: 9 Sep. 2016). The USEARCH global alignmentalgorithm was then used to map all reads, including singletons onto theremaining OTU sequences. In-house scripts were used to then group thesequences into OTUs as classified by the USEARCH global alignmentalgorithm. Individual sequences were grouped into OTUs to givemicrobiome compositional information (abundance and diversity).

High-Level Data Analysis

The Bray-Curtis dissimilarity matrix was generated for each samplepairing using the Vegan library in R 3.3.1. Dataset was visualised usingPrincipal Coordinate analysis with the Bray-Curtis dissimilarity matrix.

An in-house heatplot R function was used to generate a heatmapvisualisation with hierarchical clustering based on the Bray-Curtisdissimilarity and ward linkage.

Shannon and Simpson diversity indexes were generated using the phyloseqlibrary in R.

DESeq2 methodology was used to identify taxonomic variables that weresignificant for chosen comparisons.

Permutational MANOVA was performed on the dissimilarity matrix using theAdonis function in R.

Results

Samples from all time points were pooled for both groups (71 IBSpatients and 67 healthy controls including both the Blautix treated andplacebo groups). Analysis was performed using a distance measuregenerated on the full microbiome dataset. FIG. 1 reports that themicrobiota of IBS subjects is significantly different from that ofhealthy subjects.

Diversity analysis was carried out using Observed number of predictedTaxa (OTUs), Shannon diversity index and Simpson Diversity index. Bothtreatment groups showed an increase in diversity at Day 16 timepointwhich was significant for the observed OTUs and showed a trend for theSimpson (Raw P-value: <0.1) (FIG. 2). This increase in diversity was notobserved with patients treated with the placebo. A significant decreasein microbiota diversity was observed in the untreated IBS placebo groupbetween End of study and Day 1.

FIGS. 3A-3B report that Blautix treatment increased the microbiotanetwork connectivity of certain health-associated taxa. In healthypatients a substantial increase in inter-microbe connections wasobserved from Day 1 to Day 16 (after Blautix treatment), which suggestsan increase in cooperation and microbiota structure (FIG. 3A).Connectivity is correlated with diversity and stability. After the washperiod the network structure reverted to a network similar to thatobserved on Day 1. Blautix treatment was, therefore, able to increaseinterconnectivity in healthy patients but the effect was lost post washout. In IBS patients the network remained similar in terms ofconnectivity between Day 1 and Day 16, but an increase in connectivitywas observed by the end of the study suggesting an increased microbiotastructure post washout period in Blautix-treated IBS patients (FIG. 3B).The effect of Blautix on microbiome connectivity was, therefore, delayedin IBS patients compared to healthy patients.

Instability/change in the microbiota profiles were represented by BrayCurtis distances between time-points of the same subject. Bray-Curtisshows dissimilarity between species abundance profiles limited between0-1 (0=same; 1=do not share any species). Treatment of IBS patients withBlautix reduced the magnitude of microbiota changes during the treatment(FIG. 4A) and after the treatment (FIGS. 4B-4C). This shows that Blautixincreased the stability of the microbiota in IBS patients and that thechange continues after the intervention. This increased stability wasnot observed when IBS patients were administered the placebo (FIGS. 4A-C).

FIG. 5 reports that there was a significant increase in microbiotadiversity at the genus level for IBS patients treated with Blautix atDay 16 compared to Day 1. The diversity analysis was carried out usingthe Shannon diversity index applied to the Genus level (Rawp-value:0.04, Day 1 versus Day 16).

FIG. 6A and FIG. 6B show the changes in the mutual exclusion networks inhealthy and IBS patients after Blautix treatment. In healthy individualsthe mutual exclusion network becomes more dense and interconnected atDay 16, which is suggestive of increased competition and inhibition.This effect was lost, however, by the end of the study as the networkstructure reverted back to the initial time point during the washoutperiod (FIG. 6A). In IBS patients the effect of Blautix on mutualexclusion connectivity was to increase the network diameter over thetreatment period and the washout period. This was opposite to the effectseen in the healthy individuals where the network become denser. Duringthe washout phase for the IBS patients, multiple independentinteractions were observed that were not seen previously. Multipleindependent interactions represent pairs of taxa that are interacting ina manner that is independent of the rest of the network, i.e. they donot have any interactions to the rest of the network.

Visualisation of microbiota shows that after Blautix treatment there wasan increased network connectivity for certain health-associated taxa(FIG. 7). The health associated taxa include Clostridium cluster IV,Bifidobacterium and Prevotella. Oscillibacter is also potentially ahealth associated genera. These health-associated taxa are implicated inthe response to treatment.

Example 2—Protective Effect in Models of Neurodevelopmental Disorders

The BTBR Mouse Model

The BTBR mouse model uses inbred, genetically modified mice that displaya robust autistic-like phenotype. Deficits in social behaviours,increased repetitive behaviours and increased anxiety-related behaviourshave been reported in this strain [51]. Due to this robust behaviouralphenotype, the BTBR mouse is an ideal animal model to assess theefficacy of novel therapeutic agents for the treatment ofautistic-related behaviours. Alleviation of such symptoms by a livebiotherapeutic can also be indicative of efficacy of the biotherapeuticin the treatment of other psychiatric or neurological diseases.

Mice

Male BTBR mice were bred in house. The animals were housed in atemperature- and humidity-controlled room on a 12 hr dark cycle (lightson from 7:00-19:00 hr). All experiments were conducted in accordancewith the European Directive 2010/63/EEC, the requirements of S.I. No 543of 2012, and approved by the Animal Experimentation Ethics Committee ofUniversity College Cork.

Strain

Blautia hydrogenotrophica bacterium deposited under accession number DSM10507 and also under accession number DSM 14294.

Biotherapeutic was provided in glycerol stock. Live biotherapeutics weregrown in the facility in anaerobic conditions.

Live Biotherapeutic Administration

Dosing with Blautia hydrogenotrophica commenced when the mice were 8weeks old. These mice were treated once daily for 3 weeks via oralgavage.

Administration Schedule

The vehicle for oral administration is PBS. Daily oral administrationoccurs via oral gavage.

Fecal Collection

Fresh fecal samples were collected from individual mice before and afteradministration of Blautia hydrogenotrophica. At least 20 mg of freshfaeces were placed in a microcentrifuge tube, placed immediately on iceand then stored at −80° C.

Results

The effect of Blautix treatment on microbiota between timepoints (D14,D32) is shown in FIG. 8. Significant temporal variation in themicrobiota profiles was observed (p-value=0.001) between the beforetreatment (D14) and after treatment (D32) study timepoints.

Differential analysis using DESeq2 yielded 25 significant (adjustedp-value<0.05) differentially abundant taxa for the Blautix treatmentbetween the D14 and D32 Autism study timepoints. The taxa are listed inTable 1 below.

TABLE 1 Significant differentially abundant taxa between D14 and D32time points in the autism study. A positive fold change is interpretedas increased at D32 when compared to D14. Lowest log2 fold adjustedOTU_ID Level Classification change st error p-value 2440650 GenusClostridium XIVa 19.706 3.008 6.9E−10 307526 Species Bacteroidesacidifaciens 11.275 0.912 5.0E−33 39008 Species Bacteroides acidifaciens10.501 1.345 1.0E−13 277773 Species Alistipes finegoldii 9.954 0.9062.8E−26 1105465 Genus Barnesiella 9.255 0.923 2.8E−22 943687 FamilyPorphyromonadaceae 9.200 0.850 1.1E−25 47662 Species Barnesiellaintestinihominis 8.844 0.988 7.0E−18 181003 Genus Alistipes 8.370 2.0694.2E−04 1282905 Species Barnesiella intestinihominis 7.373 1.004 2.8E−121370810 Species Barnesiella intestinihominis 6.633 1.986 0.006 1203483Species Bacteroides acidifaciens 6.599 1.584 2.7E−04 74179 SpeciesAlistipes massiliensis 6.318 1.899 0.006 1640334 Species Barnesiellaintestinihominis 6.258 2.066 0.013 76239 Family Lachnospiraceae 6.2021.229 4.6E−06 308030 Species Barnesiella intestinihominis 6.196 1.4511.8E−04 1156020 Family Erysipelotrichaceae 5.827 1.607 0.002 712755Species Barnesiella intestinihominis 5.614 1.749 0.008 11297 FamilyPorphyromonadaceae 5.450 1.021 1.0E−06 2218722 Genus Clostridium IV3.983 1.017 0.001 594012 Species Clostridium lactatifermentans 2.9000.952 0.013 453043 Species Eubacterium ventriosum −3.675 1.260 0.018451019 Species Barnesiella intestinihominis −4.055 1.540 0.041 466087Species Akkermansia muciniphila −6.727 0.876 2.5E−13 2153421 GenusBlautia XIVa −8.051 2.577 0.010 866478 Species Barnesiellaintestinihominis −8.961 0.846 9.3E−25Summary

In a mouse model of autism in which animals were administered Blautix, asignificant variation on their microbiome was observed, including asubstantial net increase in bacterial diversity.

Example 3—Effect in Models of Cerebral Ischemia

Summary

The protective effect of Blautia hydrogenotrophica was tested in mousemodels of cerebral ischemia. To this end three groups of 5-17 mice weretested. Only normally behaving animals were included in the study. Thefirst dosing day was Day −14. One group received freeze dried bacteriadaily from the first dosing day until termination. The control groupsreceived either vehicle or lyobuffer.

On Day 1, all mice were anesthetized. A midline incision was created inthe ventral side of the neck to expose the right and left commoncarotid-arteries. A cerebral ischemia-reperfusion I/R model was theninduced by bilateral common carotid artery occlusion (BCCAO) usingvascular clips for 15 minutes. At the end of each occlusion, the clipswere removed.

Strain

Blautia hydrogenotrophica bacterium deposited under accession number DSM10507 and also under accession number DSM 14294.

Administration Schedule

Dose Volumes No. of (ml/kg or Animals Treatment Dose Level (mg/kg)ml/animal) 12 PBS n/a 10 (negative control) 17 Freeze-dried 7.8 mg in100 μl 100 μl per animal Powder 13 Freeze-dried 15.6 mg in 100 μl 100 μlper animal Bacteria (bacteria dose = 2 × 10⁸)Study Design

Days −14 to 14: Daily dose of PBS control (lyobuffer), freeze driedpowder control (vehicle) or freeze dried bacteria (Blautix).

Day 1: Cerebral ischemia-reperfusion I/R model induced by surgery.

Day 14: Half of the mice in each group were terminated.

Day 14 to 28: Daily dose of PBS control (lyobuffer), freeze dried powdercontrol (vehicle) or freeze dried bacteria (Blautix) for the remainingmice in each group.

Day 28: Termination of remaining mice.

Faecal pellets were collected at three time points: Day −14, Day 14 andDay 28. Each take was carried out in a sterile environment (fullyaseptic=cleaned between animals), with every mouse being taken out ofthe cage and placed separately into a new sterile box for individualpellet harvesting. As many pellets as possible were collected in orderto reach a minimum of 80 mg and preferably 100 mg of material per mouse.

Results

No significant differences in microbiota profiles between the Blautixtreatment, Vehicle and Lyobuffer groups were detected at D-14(p-value=0.177) before administration of Blautix (see FIG. 9A). However,significant differences were observed in microbiota profiles between thedifferent treatment groups at Day 14 (see FIG. 9B) with a p-value of0.011 observed. The inventors further assessed the temporal variation inthe microbiota of the Blautix treated group and found a significantdifference (see FIG. 9C) with a p-value of 0.002 observed.

Differential analysis using DESeq2 yielded significant (adjusted p-value<0.05) differentially abundant taxa for the Vehicle, Lyobuffer andBlautix treatment between timepoints in the Stroke study, as shown inTable 2, demonstrating a longer term impact on bacterial diversityimparted by Blautix. The taxa for the Blautix treatment are listed inTable 3, Table 4 and Table 5.

TABLE 2 Significant differentially abundant taxa between time points inthe Stroke study. D-14->D14 D14->D28 D-14->D28 Vehicle 4 0 2 Lyobuffer17 2 0 Blautix 7 14 12

TABLE 3 Significant differentially abundant taxa between D-14 and D14timepoints for the Blautix treatment in the Stroke study. A positivefold change is interpreted as increased at D14 when compared to D-14.Lowest log2 fold st adjusted OTU_ID Level Classification change errorp-value 321825 Family Ruminococcaceae 1.647 0.470 0.027 74771 SpeciesAlistipes massiliensis 1.530 0.442 0.027 567799 Genus Alistipes −1.2150.308 0.008 77091 Genus Clostridium −1.634 0.489 0.036 472737 FamilyLachnospiraceae −2.585 0.667 0.008 615246 Family Lachnospiraceae −3.0030.711 0.007 166882 Family Lachnospiraceae −5.547 1.406 0.008

TABLE 4 Significant differentially abundant taxa between D14 and D28timepoints for the Blautix treatment in the Stroke study. A positivefold change is interpreted as increased at D28 when compared to D14. ad-log2 just- Lowest fold st ed p- OTU_ID Level Classification change errorvalue 1101936 Order Clostridiales 3.275 0.709 0.001 218505 SpeciesRoseburia faecis 2.568 0.630 0.002 948888 Genus Barnesiella 2.499 0.5750.001 612631 Genus Clostridium XIVa 2.473 0.723 0.011 201398 PhylumBacteroidetes 2.045 0.605 0.011 1370810 Species Barnesiellaintestinihominis 1.878 0.579 0.016 770554 Species Alistipes putredinis1.868 0.626 0.033 558330 Genus Prevotella 1.795 0.453 0.002 943687Family Porphyromonadaceae 1.586 0.546 0.039 308030 Species Barnesiellaintestinihominis 1.324 0.361 0.005 176124 Phylum Bacteroidetes 1.1630.294 0.002 565518 Species Oscillospira guilliermondii −1.571 0.4880.016 544582 Species Flavonifractor plautii −1.599 0.569 0.050 25678Species Mucispirillum schaedleri −2.751 0.640 0.001

TABLE 5 Significant differentially abundant taxa between D-14 and D28timepoints for the Blautix treatment in the Stroke study. A positivefold change is interpreted as increased at D28 when compared to D-14.Lowest log2 fold adjusted OTU_ID Level Classification change st errorp-value 688867 Genus Clostridium XIVa 8.296 1.136 3.8E−11 612631 GenusClostridium XIVa 7.814 1.348 3.1E−07 560658 Family Lachnospiraceae 5.2411.243 0.001 929749 Species Eubacterium 3.190 0.829 0.003 ruminantium518034 Species Desulfovibrio 3.098 0.982 0.024 fairfieldensis 74771Species Alistipes 2.548 0.714 0.007 massiliensis 23310 SpeciesOdoribacter 1.621 0.475 0.011 laneus 117624 Order Clostridiales −1.7480.612 0.049 411272 Genus Clostridium XIVa −2.923 1.019 0.049 39008Species Bacteroides −2.953 0.816 0.007 acidifaciens 331352 GenusClostridium XIVa −3.969 0.626 1.6E−08 77091 Genus Clostridium −4.2471.426 0.039

Differential analysis using DESeq2 yielded significant (adjusted p-value<0.05) differentially abundant taxa for the Blautix treatment vs.Vehicle as well as Blautix treatment vs. Lyobuffer for the Stroke studytimepoints, as shown in Table 6. The taxa are listed in Table 7, Table 8and Table 9.

TABLE 6 Significant differentially abundant taxa for the Blautixtreatment in the Stroke study. D-14 D14 D28 Blautix vs. Vehicle 0 10 0Blautix vs. 2 13 0 Lyobuffer

TABLE 7 Significant differentially abundant taxa for the Blautixtreatment vs. Vehicle at D14 in the Stroke study. Lowest log2 foldadjusted OTU_ID Level Classification change st error p-value 25678Species Mucispirillum 2.604 0.688 0.014 schaedleri 3119687 FamilyLachnospiraceae 2.445 0.642 0.014 321825 Family Ruminococcaceae 2.1740.564 0.014 627 Genus Clostridium XIVa 1.915 0.601 0.043 308030 SpeciesBarnesiella −1.324 0.419 0.043 intestinihominis 1370810 SpeciesBarnesiella −1.540 0.425 0.019 intestinihominis 187271 SpeciesRuminococcus −3.475 1.065 0.042 flavefaciens 277773 Species Alistipesfinegoldii −3.751 1.178 0.043 940566 Species Staphylococcus −5.228 1.5190.026 lentus 930972 Genus Staphylococcus −5.418 1.536 0.023

TABLE 8 Significant differentially abundant taxa for the Blautixtreatment vs. Lyobuffer at D-14 in the Stroke study Lowest log2 foldadjusted OTU_ID Level Classification change st error p-value 1161472Family Lachnospiraceae 6.511 1.403 0.001 392940 Kingdom Bacteria −5.1691.346 0.022

TABLE 9 Significant differentially abundant taxa for the Blautixtreatment vs. Lyobuffer at D14 in the Stroke study ad- log2 justedLowest fold st p- OTU_ID Level Classification change error value 25678Species Mucispirillum schaedleri 2.704 0.753 0.012 1379349 GenusClostridium XIVa 2.517 0.771 0.027 742656 Species Oscillibactervalericigenes 1.738 0.459 0.009 558330 Genus Prevotella −1.634 0.4060.006 1370810 Species Barnesiella intestinihominis −1.780 0.390 0.001712755 Species Barnesiella intestinihominis −1.827 0.464 0.006 47662Species Barnesiella intestinihominis −2.109 0.606 0.014 1640334 SpeciesBarnesiella intestinihominis −2.260 0.693 0.027 1105465 GenusBarnesiella −2.306 0.627 0.010 161658 Family Lachnospiraceae −2.5650.816 0.037 277773 Species Alistipes finegoldii −3.619 1.034 0.014187271 Species Ruminococcus flavefaciens −3.924 1.057 0.010 459041Species Lactobacillus johnsonii −4.029 0.981 0.006Summary

Blautix effects a significant increase in microbiota diversitythroughout the period of the study in a mouse model of stroke, whencompared to lyobuffer or vehicle control.

Example 4—Protective Effect in Models of Neuroinflammatory Conditions

Experimental Autoimmune Encephalomyelitis (EAE) is a mouse model of CNSinflammation that mirrors many aspects of the human disease MS and EAEis the most commonly used experimental model for human MS. EAE is alsoused more generally as a model for CNS-specific autoimmune disorders[52] and for other specific conditions, including acute disseminatedencephalomyelitis. EAE is induced using immunisation with myelinpeptides and adjuvants to elicit an immune and inflammatory responsethat closely corresponds to the mechanisms underlying many autoimmuneand inflammatory disorders of the CNS, and in particular MS. Manytherapies showing efficacy in EAE have also shown efficacy in treatmentof MS in human patients [52]. Most importantly, EAE reproduces keyfeatures of MS, including inflammation, demyelination, axonal loss andgliosis. The effects of demyelination are mainly restricted to thespinal cord in EAE, with little alteration of the brain stem and thecerebellum. In EAE the CD4+ T cells are the dominant cell populationfound in the CNS.

Methodology

Blautia hydrogenotrophica (“Blautix”, strain deposited under accessionnumber DSM 10507 and also under accession number DSM 14294) was used asa freeze-dried powder and reconstituted as required.

12 adult female C57BL/6J mice were used.

On Day 0 and Day 7, animals were administered with an emulsioncontaining MOG35-55 and complete Freund's adjuvant (CFA) supplementedwith Mycobacterium Tuberculosis H37Ra by subcutaneous injections undergas (isoflurane) anaesthesia. On Day 0, two subcutaneous injections wereperformed in the flanks; one in each of the lower quadrant of the back.On Day 7, two subcutaneous injections were performed in the flanks, onein each of the upper quadrant of the back.

On Day 0 and Day 2, animals were administered with pertussis toxin (PTx)in phosphate buffered saline (PBS) by intra-peritoneal injections. OnDay 0, PTx administration was performed after MOG injections.

Treatments with Blautix or controls were administered from Day −14according to the following schedule:

-   -   Day 0: MOG/CFA, once, SC    -   Day 0: PTx, once, IP    -   Day 2, PTx, once, IP    -   Day 7: MOG/CFA, once, SC

Treatments were administered within 15 minutes of their preparation.Blautix was administered at a dose of 2×10⁸; 100 μl/mouse.

From Day 0 until the end of the experiment, animals were scored dailyfor clinical signs of EAE, including paresis and paralysis of the tailand/or limbs.

On Day −14, Day −1 and Day 34, faecal pellets were collected from eachanimal, immediately snap-frozen and stored at −80° C.

Results

The effect of Blautix treatment on microbiota between timepoints (D-14,D-1, D34) for the MS model is shown in FIG. 10. Significant temporalvariation in the microbiota profiles was observed (p-value=0.001) forthe study timepoints.

Differential analysis using DESeq2 yielded significant (adjustedp-value<0.05) differentially abundant taxa for the Blautix treatmentbetween study timepoints, as shown in Table 10. The taxa are listed inTable 11, Table 12 and Table 13.

TABLE 10 Significant differentially abundant taxa between timepoints inthe MS study. D-14->D-1 D-1->D34 D-14->D34 MS (Blautix) 42 30 58

TABLE 11 Significant differentially abundant taxa between D-14 and D-1timepoints in the MS study. A positive fold change is interpreted asincreased at D-1 when compared to D-14. Lowest log2 fold adjusted OTU_IDLevel Classification change st error p-value 1105465 Genus Barnesiella8.076 0.702 2.2E−28 48633 Genus Clostridium XIVa 7.304 0.825 7.0E−17490405 Species Turicibacter sanguinis 6.824 0.778 1.0E−16 491106 SpeciesFlavonifractor plautii 5.116 0.923 4.3E−07 43241 Genus Clostridium XIVa5.041 0.739 2.2E−10 948888 Genus Barnesiella 4.649 0.605 4.3E−13 47662Species Barnesiella intestinihominis 4.276 0.501 5.1E−16 1288839 FamilyLachnospiraceae 4.117 1.170 0.003 11297 Family Porphyromonadaceae 4.0810.600 2.2E−10 198591 Family Lachnospiraceae 3.757 0.788 2.3E−05 49543Family Lachnospiraceae 3.275 0.897 0.002 1009304 Species Oscillospiraguilliermondii 3.140 1.043 0.015 930464 Species Insolitispirillumperegrinum 2.804 1.033 0.029 1793164 Genus Parasutterella 2.720 0.5762.6E−05 1260915 Kingdom Bacteria 2.678 0.804 0.006 36112 SpeciesClostridium leptum 2.584 0.887 0.018 181003 Genus Alistipes 2.581 0.5553.3E−05 149837 Family Lachnospiraceae 2.434 0.678 0.002 1056232 GenusClostridium XIVa 2.308 0.856 0.030 770554 Species Alistipes putredinis2.223 0.556 0.001 1176501 Family Lachnospiraceae 2.079 0.758 0.028 33530Species Acetatifactor muris 1.965 0.569 0.004 43033 Genus Alistipes1.788 0.379 2.6E−05 576748 Family Ruminococcaceae 1.740 0.603 0.01950759 Species Oscillospira guilliermondii 1.570 0.409 0.001 592877Species Pseudoflavonifractor capillosus 1.512 0.418 0.002 712755 SpeciesBarnesiella intestinihominis 1.509 0.502 0.015 375558 SpeciesBarnesiella intestinihominis 1.505 0.554 0.029 307526 SpeciesBacteroides acidifaciens 1.499 0.492 0.014 74641 Species Bacteroidesacidifaciens 1.418 0.532 0.032 943687 Family Porphyromonadaceae 1.1620.397 0.018 791734 Genus Clostridium XIVa −1.064 0.377 0.023 19031Species Anaerotruncus colihominis −1.391 0.516 0.030 74179 SpeciesAlistipes massiliensis −1.810 0.305 4.7E−08 211238 Species Anaeroplasmaabactoclasticum −2.662 0.859 0.012 76239 Family Lachnospiraceae −2.7210.668 4.2E−04 743544 Genus Clostridium XIVa −3.014 0.672 7.0E−05 993522Genus Clostridium XIVa −3.394 0.708 2.2E−05 76325 Genus Lactobacillus−3.621 0.575 5.2E−09 209309 Family Lachnospiraceae −3.857 1.295 0.016567799 Genus Alistipes −5.435 0.634 4.3E−16 77091 Genus Clostridium−6.877 1.048 1.0E−09

TABLE 12 Significant differentially abundant taxa between D-1 and D34timepoints in the MS study. A positive fold change is interpreted asincreased at D34 when compared to D-1. Lowest log2 fold adjusted OTU_IDLevel Classification change st error p-value 1370810 Species Barnesiellaintestinihominis 4.794 1.196 0.001 1684470 Species Parasutterellaexcrementihominis 4.434 1.167 0.002 1070245 Species Eubacteriumplexicaudatum 3.870 0.961 0.001 518034 Species Desulfovibriofairfieldensis 3.867 0.962 0.001 1482481 Species Clostridium disporicum3.228 1.112 0.029 567799 Genus Alistipes 3.218 0.864 0.002 1404432Species Bacteroides acidifaciens 2.978 0.835 0.004 1067514 GenusBarnesiella 2.967 0.921 0.011 76325 Genus Lactobacillus 2.893 0.6830.001 307526 Species Bacteroides acidifaciens 2.218 0.351 1.8E−081288839 Family Lachnospiraceae 2.084 0.746 0.035 866478 SpeciesBarnesiella intestinihominis 1.936 0.647 0.022 23133 FamilyRuminococcaceae 1.840 0.544 0.007 472737 Family Lachnospiraceae 1.6970.524 0.011 842401 Order Clostridiales 1.601 0.535 0.022 39008 SpeciesBacteroides acidifaciens 1.494 0.390 0.002 74179 Species Alistipesmassiliensis 1.426 0.328 3.9E−04 277773 Species Alistipes finegoldii1.323 0.461 0.029 76234 Family Lachnospiraceae −1.183 0.333 0.004 948888Genus Barnesiella −1.453 0.520 0.035 150155 Family Lachnospiraceae−1.609 0.421 0.002 783115 Family Desulfovibrionaceae −2.262 0.608 0.002773427 Species Anaerotruncus colihominis −2.443 0.661 0.003 201157Family Lachnospiraceae −2.587 0.754 0.006 596894 Genus Clostridium XIVa−2.616 0.909 0.029 43033 Genus Alistipes −3.236 0.718 2.2E−04 1793164Genus Parasutterella −3.758 0.632 1.4E−07 49543 Family Lachnospiraceae−4.849 0.920 5.5E−06 490405 Species Turicibacter sanguinis −5.152 0.7042.5E−11 48282 Family Lachnospiraceae −5.460 0.666 4.7E−14

TABLE 13 Significant differentially abundant taxa between D-14 and D34timepoints in the MS study. A positive fold change is interpreted asincreased at D34 when compared to D-14. Lowest log2 fold adjusted OTU_IDLevel Classification change st error p-value 1105465 Genus Barnesiella7.221 0.754 2.1E−19 48633 Genus Clostridium XIVa 6.734 0.959 8.7E−111288839 Family Lachnospiraceae 5.820 0.811 3.5E−11 518034 SpeciesDesulfovibrio fairfieldensis 5.459 0.999 8.3E−07 1684470 SpeciesParasutterella excrementihominis 5.289 1.408 0.001 1482481 SpeciesClostridium disporicum 4.947 1.295 0.001 1370810 Species Barnesiellaintestinihominis 4.734 1.263 0.001 1070245 Species Eubacteriumplexicaudatum 4.620 0.794 1.3E−07 1067514 Genus Barnesiella 4.544 1.1032.8E−04 1575843 Species Clostridium ruminantium 4.393 1.743 0.040 43241Genus Clostridium XIVa 4.284 0.817 2.4E−06 47662 Species Barnesiellaintestinihominis 4.273 0.478 3.8E−17 1728285 Genus Lachnospiraceaincertae sedis 4.204 1.221 0.003 11297 Family Porphyromonadaceae 3.9210.577 3.4E−10 307526 Species Bacteroides acidifaciens 3.539 0.5349.9E−10 198591 Family Lachnospiraceae 3.273 0.762 1.4E−04 236126 SpeciesOscillospira guilliermondii 3.175 1.086 0.015 930464 SpeciesInsolitispirillum peregrinum 3.152 0.848 0.001 948888 Genus Barnesiella3.040 0.629 1.6E−05 491106 Species Flavonifractor plautii 3.039 1.1700.034 563211 Family Lachnospiraceae 2.564 0.965 0.030 149837 FamilyLachnospiraceae 2.562 0.890 0.016 770554 Species Alistipes putredinis2.520 0.455 6.2E−07 1260915 Kingdom Bacteria 2.505 0.677 0.001 36112Species Clostridium leptum 2.483 0.916 0.026 1056232 Genus ClostridiumXIVa 2.319 0.664 0.002 39008 Species Bacteroides acidifaciens 2.1070.274 9.9E−13 23133 Family Ruminococcaceae 2.049 0.614 0.004 74641Species Bacteroides acidifaciens 2.002 0.457 1.0E−04 712755 SpeciesBarnesiella intestinihominis 1.977 0.470 2.0E−04 277773 SpeciesAlistipes finegoldii 1.881 0.388 1.6E−05 1404432 Species Bacteroidesacidifaciens 1.805 0.563 0.006 1176501 Family Lachnospiraceae 1.6540.630 0.032 544582 Species Flavonifractor plautii 1.418 0.540 0.03276234 Family Lachnospiraceae −0.991 0.389 0.038 80190 FamilyLachnospiraceae −1.113 0.348 0.006 182471 Order Clostridiales −1.3150.472 0.021 494032 Species Clostridium oroticum −1.502 0.580 0.0342367602 Order Clostridiales −1.518 0.472 0.006 74771 Species Alistipesmassiliensis −1.617 0.408 0.001 172154 Genus Clostridium XIVa −1.6280.442 0.001 993522 Genus Clostridium XIVa −1.799 0.594 0.011 791734Genus Clostridium XIVa −1.842 0.387 2.2E−05 150155 FamilyLachnospiraceae −1.859 0.532 0.002 743544 Genus Clostridium XIVa −2.1960.558 0.001 567799 Genus Alistipes −2.378 0.513 3.9E−05 96345 GenusClostridium XIVa −2.528 0.667 0.001 19031 Species Anaerotruncuscolihominis −2.575 0.610 1.9E−04 201157 Family Lachnospiraceae −2.6150.866 0.011 578360 Family Lachnospiraceae −2.870 0.586 1.4E−05 76239Family Lachnospiraceae −3.325 0.631 2.3E−06 1165458 FamilyLachnospiraceae −3.346 0.754 8.1E−05 773427 Species Anaerotruncuscolihominis −3.475 0.776 7.0E−05 209309 Family Lachnospiraceae −3.6391.042 0.002 320120 Genus Clostridium XIVa −3.670 0.811 5.9E−05 1628488Species Vallitalea guaymasensis −4.144 1.538 0.027 48282 FamilyLachnospiraceae −4.653 1.012 4.5E−05 77091 Genus Clostridium −7.4931.192 7.9E−09Summary

Blautix effects a significant increase in microbiota diversity andresults in significant temporal variation during treatment in an animalmodel for multiple sclerosis.

The invention has been described above by way of example only and itwill be understood that further modifications may be made which fallwithin the scope of the claims.

Sequences

(Blautia stercoris strain GAM6-1 16S ribosomal RNA gene, partialsequence-HM626177) SEQ ID NO: 1    1tgcaagtcga gcgaagcgct tacgacagaa ccttcggggg aagatgtaag ggactgagcg   61gcggacgggt gagtaacgcg tgggtaacct gcctcataca gggggataac agttggaaac  121ggctgctaat accgcataag cgcacggtat cgcatgatac agtgtgaaaa actccggtgg  181tatgagatgg acccgcgtct gattagctag ttggaggggt aacggcccac caaggcgacg  241atcagtagcc ggcctgagag ggtgaacggc cacattggga ctgagacacg gcccagactc  301ctacgggagg cagcagtggg gaatattgca caatggggga aaccctgatg cagcgacgcc  361gcgtgaagga agaagtatct cggtatgtaa acttctatca gcagggaaga aaatgacggt  421acctgactaa gaagccccgg ctaactacgt gccagcagcc gcggtaatac gtagggggca  481agcgttatcc ggatttactg ggtgtaaagg gagcgtagac ggaagagcaa gtctgatgtg  541aaaggctggg gcttaacccc aggactgcat tggaaactgt ttttcttgag tgccggagag  601gtaagcggaa ttcctagtgt agcggtgaaa tgcgtagata ttaggaggaa caccagtggc  661gaaggcggct tactggacgg taactgacgt tgaggctcga aagcgtgggg agcaaacagg  721attagatacc ctggtagtcc acgccgtaaa cgatgaatac taggtgttgg ggagcaaagc  781tcttcggtgc cgcagcaaac gcaataagta ttccacctgg ggagtacgtt cgcaagaatg  841aaactcaaag gaattgacgg ggacccgcac aagcggtgga gcatgtggtt taattcgaag  901caacgcgaag aaccttacca agtcttgaca tcgatctgac cggttcgtaa tggaaccttt  961ccttcgggac agagaagaca ggtggtgcat ggttgtcgtc agctcgtgtc gtgagatgtt 1021gggttaagtc ccgcaacgag cgcaacccct atcctcagta gccagcaggt gaagctgggc 1081actctgtgga gactgccagg gataacctgg aggaaggcgg ggacgacgtc aaatcatcat 1141gccccttatg atttgggcta cacacgtgct acaatggcgt aaacaaaggg aagcgagccc 1201gcgaggggga gcaaatccca aaaataacgt cccagttcgg actgcagtct gcaactcgac 1261tgcacgaagc tggaatcgct agtaatcgcg aatcagaatg tcgcggtgaa tacgttcccg 1321ggtcttgtac acaccgcccg tcacaccatg ggagtcagta acgcccgaag tc(Blautia wexlerae strain WAL 14507 16S ribosomal RNA gene, partial sequence-EF036467) SEQ ID NO: 2    1caagtcgaac gggaattant ttattgaaac ttcggtcgat ttaatttaat tctagtggcg   61gacgggtgag taacgcgtgg gtaacctgcc ttatacaggg ggataacagt cagaaatggc  121tgctaatacc gcataagcgc acagagctgc atggctcagt gtgaaaaact ccggtggtat  181aagatggacc cgcgttggat tagcttgttg gtggggtaac ggcccaccaa ggcgacgatc  241catagccggc ctgagagggt gaacggccac attgggactg agacacggcc cagactccta  301cgggaggcag cagtggggaa tattgcacaa tgggggaaac cctgatgcag cgacgccgcg  361tgaaggaaga agtatctcgg tatgtaaact tctatcagca gggaagatag tgacggtacc  421tgactaagaa gccccggcta actacgtgcc agcagccgcg gtaatacgta gggggcaagc  481gttatccgga tttactgggt gtaaagggag cgtagacggt gtggcaagtc tgatgtgaaa  541ggcatgggct caacctgtgg actgcattgg aaactgtcat acttgagtgc cggaggggta  601agcggaattc ctagtgtagc ggtgaaatgc gtagatatta ggaggaacac cagtggcgaa  661ggcggcttac tggacggtaa ctgacgttga ggctcgaaag cgtggggagc aaacaggatt  721agataccctg gtagtccacg ccgtaaacga tgaataacta ggtgtcgggt ggcaaagcca  781ttcggtgccg tcgcaaacgc agtaagtatt ccacctgggg agtacgttcg caagaatgaa  841actcaaagga attgacgggg acccgcacaa gcggtggagc atgtggttta attcgaagca  901acgcgaagaa ccttaccaag tcttgacatc cgcctgaccg atccttaacc ggatctttcc  961ttcgggacag gcgagacagg tggtgcatgg ttgtcgtcag ctcgtgtcgt gagatgttgg 1021gttaagtccc gcaacgagcg caacccctat cctcagtagc cagcatttaa ggtgggcact 1081ctggggagac tgccagggat aacctggagg aaggcgggga tgacgtcaaa tcatcatgcc 1141ccttatgatt tgggctacac acgtgctaca atggcgtaaa caaagggaag cgagattgtg 1201agatggagca aatcccaaaa ataacgtccc agttcggact gtagtctgca acccgactac 1261acgaagctgg aatcgctagt aatcgcggat cagaatgccg cggtgaatac gttcccgggt 1321cttgtacaca ccgcccgtca caccatggga gtcagtaacg cccgaagtca gtgacctaac 1381tgcaaagaag gagctgccga aggcgggacc gatgactggg gtgaagtcgt aacaaggt(consensus 16S rRNA sequence for Blautia stercoris strain 830)SEQ ID NO: 3TTTKGTCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAGCGAAGCGCTTACGACAGAACCTTCGGGGGAAGATGTAAGGGACTGAGCGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCTCATACAGGGGGATAACAGTTGGAAACGGCTGCTAATACCGCATAAGCGCACAGTATCGCATGATACAGTGTGAAAAACTCCGGTGGTATGAGATGGACCCGCGTCTGATTAGCTAGTTGGAGGGGTAACGGCCCACCAAGGCGACGATCAGTAGCCGGCCTGAGAGGGTGAACGGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAAGGAAGAAGTATCTCGGTATGTAAACTTCTATCAGCAGGGAAGAAAATGACGGTACCTGACTAAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGAAGAGCAAGTCTGATGTGAAAGGCTGGGGCTTAACCCCAGGACTGCATTGGAAACTGTTTTTCTTGAGTGCCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAATACTAGGTGTTGGGGAGCAAAGCTCTTCGGTGCCGCAGCAAACGCAATAAGTATTCCACCTGGGGAGTACGTTCGCAAGAATGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTATTCGAAGCAACGCGAAGAACCTTACCAAGTCTTGACATCGATCTGACCGGTTCGTAATGGAACCTTTCCTTCGGGACAGAGAAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTATCGTCAGTAGCCAGCAGGTAAAGCTGGGCACTCTGAGGAGACTGCCAGGGATAACCTGGAGGAAGGCGGGGACGACGTCAAATCATCATGCCCCTTATGATTTGGGCTACACACGTGCTACAATGGCGTAAACAAAGGGAAGCGAGCCCGCGAGGGGGAGCAAATCCCAAAAATAACGTCCCAGTTCGGACTGCAGTCTGCAACTCGACTGCACGAAGCTGGAATCGCTAGTAATCGCGAATCAGAATGTCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTCAGTAACGCCCGAAGTCAGTGACCCAACCTTAGGGAGGGAGCTGCCGAAGGCGGGATTGATAACTGGGGTGAAGTCTAGGGGGT(consensus 16S rRNA sequence for Blautia wexlerae strain MRX008)SEQ ID NO: 4TTCATTGAGACTTCGGTGGATTTAGATTCTATTTCTAGTGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCTTATACAGGGGGATAACAGTCAGAAATGGCTGCTAATACCGCATAAGCGCACAGAGCTGCATGGCTCAGTGTGAAAAACTCCGGTGGTATAAGATGGACCCGCGTTGGATTAGCTTGTTGGTGGGGTAACGGCCCACCAAGGCGACGATCCATAGCCGGCCTGAGAGGGTGAACGGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAAGGAAGAAGTATCTCGGTATGTAAACTTCTATCAGCAGGGAAGATAGTGACGGTACCTGACTAAGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGTGGCAAGTCTGATGTGAAAGGCATGGGCTCAACCTGTGGACTGCATTGGAAACTGTCATACTTGAGTGCCGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAATACTAGGTGTCNGGGGAGCATGGCTCTTCGGTGCCGTCGCAAACGCAGTAAGTATTCCACCTGGGGAGTACGTTCGCAAGAATGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAAGTCTTGACATCCGCCTGACCGATCCTTAACCGGATCTTTCCTTCGGGACAGGCGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTATCCTCAGTAGCCAGCATTTAAGGTGGGCACTCTGGGGAGACTGCCAGGGATAACCTGGAGGAAGGCGGGGATGACGTCAAATCATCATGCCCCTTATGATTTGGGCTACACACGTGCTACAATGGCGTAAACAAAGGGAAGCGAGATCGTGAGATGGAGCAAATCCCAAAAATAACGTCCCAGTTCGGACTGTAGTCTGCAACCCGACTACACGAAGCTGGAATCGCTAGTAATCGCGGATCAGAATGCCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTCAGTAACGCCCGAAGTCAGTGACCTAACTGCAAAGAAGGAGCTGCCGAA(Blautia hydrogenotrophica strain S5a36 16S ribosomal RNA gene, partialsequence-X95624.1) SEQ ID NO: 5    1gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac gaagcgatag agaacggaga   61tttcggttga agttttctat tgactgagtg gcggacgggt gagtaacgcg tgggtaacct  121gccctataca gggggataac agttagaaat gactgctaat accgcataag cgcacagctt  181cgcatgaagc ggtgtgaaaa actgaggtgg tataggatgg acccgcgttg gattagctag  241ttggtgaggt aacggcccac caaggcgacg atccatagcc ggcctgagag ggtgaacggc  301cacattggga ctgagacacg gcccaaactc ctacgggagg cagcagtggg gaatattgca  361caatggggga aaccctgatg cagcgacgcc gcgtgaagga agaagtatct cggtatgtaa  421acttctatca gcagggaaga aagtgacggt acctgactaa gaagccccgg ctaattacgt  481gccagcagcc gcggtaatac gtaaggggca agcgttatcc ggatttactg ggtgtaaagg  541gagcgtagac ggtttggcaa gtctgatgtg aaaggcatgg gctcaacctg tggactgcat  601tggaaactgt cagacttgag tgccggagag gcaagcggaa ttcctagtgt agcggtgaaa  661tgcgtagata ttaggaggaa caccagtggc gaaggcggcc tgctggacgg taactgacgt  721tgaggctcga aagcgtgggg agcaaacagg attagatacc ctggtagtcc acgctgtaaa  781cgatgaatac taggtgtcgg gtggcaaagc cattcggtgc cgcagcaaac gcaataagta  841ttcccacctg gggagtacgt tcgcaagaat gaaactcaaa ggaattgacg gggacccgca  901caagcggtgg agcatgtggt ttaattcgaa gcaacgcgaa gaaccttacc aaatcttgac  961atccctctga ccgggaagta atgttccctt ttcttcggaa cagaggagac aggtggtgca 1021tggttgtcgt cagctcgtgt cgtgagatgt tgggttaagt cccgcaacga gcgcaaccct 1081tattcttagt agccagcagg tagagctggg cactctaggg agactgccag ggataacctg 1141gaggaaggtg gggatgacgt caaatcatca tgccccttat gatttgggct acacacgtgc 1201tacaatggcg taaacaaagg gaagcgaagg ggtgacctgg agcaaatctc aaaaataacg 1261tctcagttcg gattgtagtc tgcaactcga ctacatgaag ctggaatcgc tagtaatcgc 1321gaatcagaat gtcgcggtga atacgttccc gggtcttgta cacaccgccc gtcacaccat 1381gggagtcagt aacgcccgaa gtcagtgacc caaccnaaag gagggagctg ccgaaggtgg 1441gactgataac tggggtga

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The invention claimed is:
 1. A method comprising administering to asubject a pharmaceutical composition that comprises: a bacteria strainof the species Blautia hydrogenotrophica comprising 99.5% sequenceidentity to the polynucleotide sequence of SEQ ID NO:5 as determined bya Smith-Waterman homology search algorithm using an affine gap searchwith a gap open penalty of 12, a gap extension penalty of 2, and aBlocks Substitution Matrix (BLOSUM) of 62 and a pharmaceuticallyacceptable excipient, diluent, or carrier, wherein the administeringresults in an increase in an amount of Oscillibacter valericigenes andBarnesiella intestinihominis and a decrease in an amount of a bacteriafrom the genus Lachnospiraceae in the gastrointestinal tract of thesubject relative to an amount of the respective bacteria prior to theadministering, as determined by bacteria count in feces.
 2. The methodof claim 1, wherein the bacteria strain comprises a polynucleotidesequence of a 16S rRNA gene that has polynucleotide sequence of SEQ IDNO:
 5. 3. The method of claim 1, wherein the subject is human.
 4. Themethod of claim 1, wherein the administering is oral.
 5. The method ofclaim 1, wherein the pharmaceutical composition is a solidpharmaceutical composition.
 6. The method of claim 1, wherein thebacteria strain is active.
 7. The method of claim 1, wherein thepharmaceutical composition is an enteric formulation.
 8. The method ofclaim 1, wherein the pharmaceutical composition is encapsulated in oneor more capsules.
 9. The method of claim 1, wherein the pharmaceuticalcomposition comprises an antioxidant.
 10. The method of claim 1, whereinthe pharmaceutical composition comprises from about 1×10⁹ to about1×10¹² CFU of the bacteria strain.
 11. The method of claim 1, whereinthe pharmaceutical composition comprises from about 1×10³ to about1×10¹¹ CFU/g of the bacteria strain with respect to total weight of thepharmaceutical composition.
 12. The method of claim 1, wherein theadministering comprises providing one or more doses of 1 g, 3 g, 5 g or10 g of the pharmaceutical composition.
 13. The method of claim 1,wherein the subject has less than 99 different bacterial species and/orless than 190 different bacterial strains in its microbiota.
 14. Themethod of claim 1, wherein the subject has less microbiotic diversity orstability relative to a healthy subject, as determined by a Shannondiversity index.
 15. The method of claim 1, wherein the subject has oneor more of irritable bowel syndrome, irritable bowel disorder, obesity,or type 2 diabetes.
 16. The method of claim 1, further comprisingadministering an additional therapeutic agent to the subject.
 17. Themethod of claim 1, wherein at least 50% of the bacteria strain asmeasured by an amount of CFU, remains viable after about 1 year ofstorage when the pharmaceutical composition is stored in a closedcontainer at 25° C. at 95% relative humidity.